Just because Japan doesn't lash out at every provocation doesn't mean it is a weak country.
For instance, Israel. Every time a rocket is fired into a settlement, the IDF initiate aggressive military responses, far outweighing the level of the initial enemy attack. What does this achieve? Escalated conflict.
Japan's international stance is a balance between a desire to correct what it sees as 'wrongs' (the northern Islands, Dokdo, the oilfields, etc) and its World #2 economic status. To overtly challenge the status quo would inevitably devastate its regional and global economic position.