Authorities are searching for an unknown number of passengers and pilots after an aircraft crashed into the water off Western Australia.

Police were alerted to a privately owned sea plane that plunged near Thomson Bay on Rottnest Island shortly after taking off about 4pm (7pm AEST) today.

Witnesses told 9News the aircraft stalled, rocking from side to side before the left wing hit the water.

The plane could be seen half-submerged in the water as police and nearby boaties responded.

Police Commissioner Col Blanch said four people had been recovered from the water but the total number of pilots or passengers inside the plane when it crashed was still unknown.

9News understands up to six people were on board.

Two women in their 40s were seriously injured and were awaiting a rescue helicopter to be flown to Perth Hospital.