Only sitting down is no problem. Otherwise, the handshake is globally accepted body language for greeting among the people
Further explanation -
Bowing means doing Ruku (putting at 90 degrees) or doing prostrating means doing Suju (completely down, putting your fore-head down) is Haram (not allowed) in Islam. You can only bow down and do Suju to Allah (God) and no one else.
Sitting down is not Haram. But a person you want to show as superior and want to degrade you and sit down i.e. not good in Islam. This is against to Islamic culture. All the human being are equal in Islamic culture.
Allah said in Surah Al Hujuraat Ayat (Quran Ch.49 V.13) -
"Human beings, We created you all from a male and a female, and made you into nations and tribes so that you may know one another. Verify the noblest of you in the sight of Allah is the most God-fearing of you. Surely Allah is All-knowing, All-Aware."
In short, you can sit down to greet the people in Japan.
Japanese people are friendly, they can understand the fact that the greetings against the religion's rule is prohibited and it will not be considered as disrespectful act. Here, your intention behind 'not bowing' is pure and there is specific reason. You have respect for them in your mind and that solves the problem.
The handshake is globally accepted body language.