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I was surprised when I first came to the Japanese school system here in Hokkaido too. Most every teacher drinks, but not necessary like fish. Out of politeness, I drank for the first few months. But, being an adult (and that I don't like drinking), I decided to make the decision for myself, and quit completely. Japanese culture strongly encourages conformity, but its not so radically different than in America or elsewhere. However, I've noticed that while people here in Japan are more likely to encourage foreigners to drink to kick back, have fun, and socialize, they also usually respect (and anticipate) lifestyle differences. Vegetarianism, quitting alcohol, and abstaining from formalities* may frustrate/confuse some Japanese people, but you shouldn't be concerned with every detractor (just like anywhere else, you can't please everyone). These are personal choices, made for personal, well-meaning reasons (I hope). As long as you stick to your customs and life decisions, people will respect them. Will the die-hard super drinkers avoid you? Likely yes, but I think you're better off not drinking if you don't want to. I still go out with my Japanese coworkers and friends when they drink, and I drink Cola or ice tea.
*By the way, I recommend using basic formalities (simple keigo, bowing) where appropriate, and as you can. If you can't, you can't.