alex32 Flarum supports any algorithm supported by PHP's password_hash. Flarum uses bcrypt, but if you store a hash for another compatible algorithm it will work out of the box as well because the algorithm name is stored in the hash itself.
If you create users via the REST API, the password must be sent in plain text though.
If you are managing login without going through Flarum's /login or /api/token endpoints, you can just set the password to any random value when creating the user, or even leaving the password column empty, and programmatically create login tokens for each users.