Let me start this piece with the understatement of the century -- there are huge differences between Japanese culture and Western culture.
Because of this, even when we Western tourists believe ourselves to be on our best behavior when traveling in Japan, we can still make numerous social faux-pas and unintentionally annoy or offend the locals. While the habits of a lifetime can be difficult to break, having a bit of insight into the type of behaviors that Japanese people tend to find jarring will go a long way towards finding favor on your trip.
What Offends Japanese The Most?

1. Being too noisy
This is probably the most common one I’ve come across. Many of us foreigners have no idea how loud our “indoor voices” actually are compared to the average volume of a Japanese person!
This issue is particularly important when traveling by train. In many Western cities, having loud conversations or sharing a laugh on public transport is commonplace – but it really isn’t the done thing in Japan. If you absolutely must speak to your friends on the train, a whispered tone is best. If you have an issue with not talking, I suggest bringing a pair of headphones with you and listen to music or a podcast to keep yourself occupied.
Restaurants and public baths are other places where foreigners fall into the trap of being too noisy. While at home, going out for a meal or a pamper day with your friends might be an excuse to let loose and be animated, in Japan these are quiet tranquil experiences. Disturbing the peace of others in these settings will not put you in the good books!
This also counts for eating noisily - slurping and loud chewing are big no-no's in Japan.

2. Being confrontational
Direct conflict isn’t part of Japanese culture. If you’re an assertive person who is used to putting in complaints about services or facilities that you find fault with, you might have to bite your tongue while in Japan.
There are ways and means of making complaints – but they usually involve putting something in writing to a management company and entering into a lengthy correspondence, rather than directly telling a person you are dealing with that you are unhappy.
This avoidance of confrontation goes both ways. Even if you really annoy a Japanese person, they’re unlikely to show any outward signs of being disgruntled - which makes it extra important to do your research on social norms! If you're perplexed by how the Japanese keep the peace, I recommend reading this book for a better understanding of this.

3. Openly talking about drug use
Many of us foreigners have a casual attitude to drug use. If you look at Western culture, a lot of our popular music, TV, and films reference illegal drugs, and many Westerners are open about their own drug experimentation.
I’m going to say this very explicitly – do not talk about illegal drug use to Japanese people. It doesn’t matter if you’re enjoying a drink or a smoke with them and you feel the mood is right to bring up a hilarious story about a bad trip you once had – the topic is taboo in a way that foreigners struggle to conceptualize. Drug users are seen as addicts and criminals, and are shunned by society – this isn’t the type of impression you want to give people of yourself when in Japan.

4. Violating personal space
If you’re a hugger, this is something to be aware of. The vast majority of Japanese people do not stand close to each other and do not touch affectionately when in public.
While you might think you’re showing warmth by offering a hug or a pat on the back to your new Japanese friend, you’re in fact putting them into a very uncomfortable situation. Even a handshake can be over-stepping the line for many – if in doubt, use the bow greeting.

5. Tardiness
You can take it from a woman who once showed up a whole three minutes late to a guided tour and nearly gave the poor tour guide a stroke – punctuality is a huge thing in Japan, and virtually nobody is late for anything. Everybody that I know in Japan owns a physical watch. I highly recommend getting a smartwatch if you plan on staying here.
While in Western society it might be acceptable to arrive five or ten minutes late to meet somebody, this is considered hugely disrespectful in Japan – and is a pretty sure-fire way to instantly annoy a Japanese person.
In the same vein, the Japanese tend to be very organized in their social planning. They’ll likely be frustrated by you if you try to make flexible plans, such as “meet around lunchtime”. Pick an exact time with plenty of advance notice, and stick to it!

6. Staring
This one is important. For many foreigners, eye contact is considered polite – it shows we are actively listening to someone. Most of us would have been scolded growing up if we didn’t maintain eye contact with others in conversation.
In Japan, this is the opposite. Direct eye contact is considered “staring”, and is perceived as rude and intimidating. Making eye contact in Japan is one of the easiest ways to do something pretty disrespectful when you’re actually trying to be polite.

7. Pointing
I’m very guilty of doing this one without thinking of the consequences, especially when trying to overcome a language barrier. While pointing at something to try and communicate might seem like an efficient way to get across what you’re talking about, it’s considered very rude behavior in Japan. Even pointing at yourself can be jarring to a Japanese person.
If you must use a physical gesture, gently gesture towards the object using a wave of the whole hand rather than isolating your finger.

8. Leaving shoes on indoors
Japanese households operate a strict no shoes indoors rule for hygiene and cleanliness reasons. If you walk into a Japanese house in your muddy shoes, this is one situation where your host probably will overcome the awkwardness and say something to you – they just won’t be able to stand it! If you aren't comfortable with leaving your shoes outside, get yourself a big backpack and throw those suckers in there.
If you’re a guest in a Japanese home, save your host the stress of this encounter by removing your shoes the minute you cross the threshold.

9. Wearing toilet slippers outside of the toilet room
Look, I probably didn’t have to include this very specific point because it’s obvious to most, but I made this mistake the first time I visited Japan and I need to ensure that nobody else in the world does, ever.
I was a tired young backpacker, and I checked into my hotel distraught at the fact one of my cheap sandal straps had snapped off during the walk from the train. Imagine my delight when I saw my hotel room included a free pair of what I thought were flip flops!
When I threw them on and wandered down to reception to ask a question, even the exceptionally polite Japanese staff couldn’t hide the look of horror on their faces upon seeing a foreigner strolling up to them in toilet slippers.
Don’t be that person.

10. Looking unkempt
This one’s for all the backpackers out there. Appearance is very important to Japanese people – and you’ll rarely see a Japanese person go out in public when they’re not immaculately dressed and groomed.
As such, wandering the streets with un-brushed hair, stained clothes, and that distinctive musty backpacker smell that we’re all capable of something will earn you a few…looks, to say the least! Every time I'm traveling across Japan, I keep a travel grooming kit with me.

11. Smoking outside designated areas
Rates of smoking are high in Japan, but that doesn’t mean you can light up whenever and wherever you see fit. Smoking is only permitted in designated areas – you can’t miss these, they’re literally glass enclosures labeled as “smoking area”.
If you smoke in any other public place, not only are you being annoying – you’re also breaking the law. See this post for more information on smoking etiquette in Japan.

12. Not being private enough about bodily functions
Maybe you burp after eating at home, and your friends think it’s funny. I guarantee you, you will not get a laugh in Japan – burping is considered extremely rude. Flatulence likewise – you’re expected to do these things somewhere private.
This guideline extends to toilet etiquette. Many Japanese toilets make noises specially designed to cover the sound of anything you might be doing in the cubicle – and you’re expected to leave the toilet itself looking as clean as when you entered. If you don’t already observe these rules anyway, they might be good souvenirs to bring home with you!
Also worth noting, blowing your nose in public in Japan is considered really gross. You’ll be saving yourself and others a lot of embarrassment if you find a private place, like a toilet cubicle, to do this.

13. Not using a mask while sick
For many foreigners, going about their daily routines with a common cold or a sore throat isn’t an issue. In Japan, you are expected to protect others from your germs by wearing a mask when you’re feeling unwell. I suggest buying a box of masks or get reusable ones if you're coming to Japan.
If you go out without a mask and proceed to complain about symptoms to your Japanese friend, they’ll likely be annoyed at your recklessness in exposing them to your illness.

14. Breaking the rules
I must say, I’m with the Japanese on this one. The Japanese as a race are very respectful of rules. Pulling stunts like skipping queues, or trying to enter sites without paying, or any other way you might try to pull the wool over someone’s eyes to benefit yourself – just really not cool in Japan.
Now one situation where you might genuinely do this accidentally is waiting for a train – when the train pulls up, you might think that it’s okay for everyone to just enter as they wish, as is the case in many Western public transport systems. No, you are expected to follow the queueing system and patiently wait until those in front of you have boarded first.
While you might not be explicitly called out, be aware that if you ever skipped someone in a queue in Japan, they knew – and they were mad.

15. Littering
Again, this is something that hopefully none of us do at home, either – but littering is particularly unacceptable in Japanese society. It’s also worth noting that there are particular bins for baby nappies (you can find these in public toilets) and you’re expected to bring your dog’s waste home to your own bin.

16. Poor hygiene practices in public bathing
If you’re visiting a public bath, you might think this is your opportunity to get clean. Actually, you’re expected to be clean before you enter the bath to avoid sullying the water.
Be sure to take a shower onsite at the public bath before entering the communal water – and not just a quick dip under the spray, a thorough scrub. If you don’t the people you’re sharing the bath with will be majorly grossed out.

17. PDA
If you’re traveling Japan as a couple, this is something to be aware of. Public displays of affection, such as kissing in public, are extremely out of the ordinary in Japan. There’s an urban myth I’ve heard a few times that kissing in public is illegal in Japan – it’s actually not, just massively disapproved of. Don’t do it!

18. Leaving food on the plate
In accordance with the Japanese practice of Mottaini (leaving no waste), giving back a plate with food still on it is seen as extremely rude. This is particularly true if you have the honor of dining in a Japanese home – to give back food would be perceived as you not enjoying the offering.
Bear this in mind if you’re ever dining in a buffet or banquet style in Japan – only take what you’re sure you can eat to avoid offending the cook.

19. Pouring soy sauce over rice
For many of us foreigners, this is the first thing we do when we get a plate of plain rice – drown it with delicious soy sauce. I know this is what I did the first few times I ate out in Japan, and I cringe at the thoughts of it now.
The little dish beside your bowl is for soy sauce – pour the soy in there, and dip your rice as you wish.

20. Bad chopstick manners
When you finish eating or are taking a break, place your chopsticks to the side of the plate. Chopsticks coming vertically out of a dish is part of a funeral ritual, and seeing this will make your Japanese companions cringe.

21. Refilling your own glass
If you’re out eating with friends, it is polite to refill their glasses as in Western culture (just make sure you use both hands to hold the bottle). The difference in Japan is it is considered rude to refill one’s own glass. Instead, put the bottle down when you get to your own glass and one of your companions will refill it.

22. Tipping
While not tipping in restaurants is rude in many Western cultures, tipping is rude in Japanese culture. Don’t be that foreigner that tries to insist on your server or guide accepting extra money – while your actions are no doubt well-intentioned, you might be deeply offending them.

Try Your Best
As you can probably tell from this post if you’re not used to Japanese culture you’re definitely going to make some mistakes that will annoy those around you. There are so many intricacies to Japan that are hard to wrap your head around, even when you’ve done in-depth research.
If it’s your first time in Japan, you’re going to do a lot of learning on the job – but once you make a big faux-pas once, you’ll know not to repeat it again (a prime example being young Nicola and the toilet slippers). The key thing is to be well-intentioned and well-informed – this will minimize awkwardness for both you and the locals you deal with.