Government troops backed by naval gunships and armored vehicles Friday stormed a police building occupied by renegade Moslem officers after the rebels killed a military commander they took hostage 28 hours earlier, officials said.

The fierce fighting raged for 31/2 hours at the regional police headquarters of Zamboanga Province, 500 miles south of Manila, before military officials ordered a suspension of operations until dawn.Officials said at least three soldiers and three civilians were wounded outside the camp. They expected the casualty figures to rise once they complete the operation and survey the damage at daybreak.

Defense Secretary Fidel Ramos told reporters in Manila the assault was launched after government negotiators confirmed fears that the regional police commander, Brig. Gen. Eduardo Batalla, had been killed earlier.

Batalla and Col. Romeo Abendan, his chief of staff, were taken hostage shortly before noon when they attempted to arrest the renegade officers in connection with the 1984 assassination of the Zamboanga mayor.

The fate Abendan was not clear. Ramos said Abendan refused an offer by the Moslems to release him, saying he wanted to stay with Batalla, not knowing that Batalla had died.

Ramos said military officials decided to break the impasse after government negotiators reported that "no more favorable results could be achieved by negotiations."

Radio news reports said the body of Batalla had been retrieved, but the broadcasts could not be confirmed immediately.