It is all part of the breaking in process. It needs to be done at the first service (500 miles if I recall), and then you get the normal 5000 miles or whatever between valve clearance checks.
This is from the Ninja 250 faq (faq.ninja250.org). The Ninja 500 and 250 engine are very similar. Frankly, this applies to most bike engines.
“Do you have to do each and every one of them? Yes. Each and every one.
If you find a mechanic who says they’ll do the 500 mile inspection for what seems like a suspiciously low price, confirm that they will actually check the valves (which is very time consuming), get it in writing, and get the results of that check in writing (they should list clearances for each valve, even if it’s just a “good/no good” type of listing) when they’re done. If you don’t see the results of the valve check, hold them to their written statement. It must be done. Some bikes are fine at 500 miles, but others definitely need adjustment, and waiting until 6000 miles could damage your engine.
The valves in the engine are the component which seals the combustion chamber, and allows your engine to make power. If they’re not adjusted properly, you get one of several results: 1. the engine makes less power; 2. the engine makes less power and destroys the valves (a $500+ repair); 3. the engine makes a lot less power (or no power) and destroys big chunks of itself. The third outcome is admittedly unlikely, but it is within the realm of possibility, even at 500 miles on the odometer.
Nearly every owner who has done their own valves at 500 miles has reported that some, or all, of the valves were tight. If your dealer says you don’t need to do a valve check at 500 miles, he’s either blowing you off or is clueless. In either case you should find someone else to work on your bike, such as a good, independent mechanic. “