All but one of the chakra gates are story related and each big area has one. So you will come across them eventually normally playing the game.
The last one is beside the point of no return of the game.
So instead of leaving for the final encounter by doing your new special move walk further to the right and there will be the last chakra gate.
So really easy to find
6th one may be optional as well but you come across it during the story, not sure if you can progress the story without it. Will see if I have a save there to check but if anybody else can confirm that please post in the comments.