Two men have been injured and Australia's largest sail-training ship has been damaged in a collision at a Perth port.

A large container ship, the Maersk Shekou, was pushed into the STS Leeuwin after being struck by a sudden squall as it entered Fremantle Port after 6am on Friday.

Two night watch crew members on board the Leeuwin suffered injuries and were taken to hospital. 

Fremantle Ports said the collision damaged the sailing boat's masts and superstructure, but the hull appeared to not have sustained major damage.

The bow of the 332-metre Shekou struck the Leeuwin first, with the stern of the vessel then hitting A Berth and the roof of the Maritime Museum.