In the episode "Message in a Bottle", when the EMH and EMH-2 take over the U.S.S Prometheus, EMH-2 says "Taking power from life supports-we don't need that."
But later, two Starfleet people beam aboard, with no life supports on,and survive.
Also, the Promethus will not let the EMH view info on the Multi-Vector Assault Mode at his clearing, but will let him actually use it, even though he doesn't have clearence to even find out about it.