What Ninja (250, 600, 650, etc)? How many miles? Is it carbureted or EFI?
Usually a loss of power once an engine gets up to temp will point to things like the valve lash being tight, especially when it runs good cold. Clogged jets tend to not run good cold worse than hot, so I wouldn't put my money on it being the carb(s) if it is indeed carbureted. That doesn't mean it couldn't be carburetor related. Clogged air passages and rubber diaphragms that harden with age can cause all sorts of weird issues. Any condition that would cause it to go rich would present itself as running good cold and then poorly when hot. You would have to do a plug chop and check the plug(s) to see if it is indeed rich.
If it's an EFI bike, again, start with valve lash, and then start looking into sensors. It could be a faulty knock sensor or temp sensor and the ECU is pulling timing trying to save the engine from damage.