Pro-Russian troops have stormed the Ukrainian navy headquarters in the Crimean port of Sevastopol and reportedly detained the navy chief a day after Russian president Vladimir Putin signed a treaty with local authorities to annex the region.

A representative of the pro-Russian forces claimed that the head of the Ukrainian navy, Serhiy Hayduk, had been captured.

"He was blocked and he had nowhere to go. He was forced out and he has been taken away," Igor Yeskin said.

There were reports that Hayduk was led away by the Russian Federal Security Service. The information was not immediately confirmed by Ukraine.

About 200 Crimean self-defence forces backed by armed men, believed to be Russian servicemen, burst through the base gates using an ambulance car.

Troops on site did not resist and no shots were fired, despite defence ministry authorisation that force could be used for self-defence, after a soldier was killed in a similar incident in Simferopol on Tuesday.

The invaders replaced the Ukrainian flag in the parade ground by the headquarters building with a Russian flag.

Ukrainian navy spokesman Sergiy Bogdanov told AFP that officers barricaded themselves inside a building. Later, some Ukrainian servicemen were seen leaving the base to the cheering of the invading force.

The attackers, some wearing balaclavas, removed a safe from the naval building.