Ukrainian servicemen filed out of navy headquarters in Sevastopol on Wednesday with tears in their eyes after the base was seized by pro-Moscow militants, Russian troops and Cossack forces.

The assault began when some 200 unarmed militants -- some of them in balaclavas -- sawed through a fence and overran the base before heavy heavily armed Russian troops and Cossacks arrived on the scene.

Ukrainian sailors were seen leaving their barracks without their weapons and taking a few belongings with them as uniformed Russian soldiers with rifles patrolled the gate.

"We have been temporarily disbanded and everyone now has to make a choice" -- serve the new pro-Moscow government of Crimea or leave the peninsula altogether, one sailor, Vlad, told AFP as he walked away in his military uniform with lieutenant chevrons.

"I was born here and I grew up here and I have been serving for 20 years. Where am I going to go?" said Vlad, one of an estimated 22,000 Ukrainian military personnel stranded in Crimea as it transitions to Russian rule.

"These are Russian soldiers, most likely special forces. I have been serving a long time, I know what Russian special forces look like," he said of the troops now controlling the headquarters.

"We cannot use guns here. We don't need a conflict," he said, despite orders from the Kiev government that soldiers in Crimea can use their weapons for "self-defence".

Asked whether he is quitting the Ukrainian army, he said no.

"I'm leaving for a while... while time passes and while our superiors make a decision."

Women were waiting for the officers outside, loading the hastily stuffed plastic bags into cars.

A few soldiers were seen gingerly carrying out their parade naval coats.

"We will come back for the rest tomorrow if they allow us," one said.

A pro-Russian crowd with Russian flags outside the headquarters clapped when two dozen pro-Russian militia marched out of the premises and formed a a line before a commander who thanked them to the cries of "Hurray!".

- 'I am not a partisan' -

The Ukrainian servicemen looked on warily. "Some of them believe in what they are doing, some are FSB (Russian Federal Security Service), and some are just looting," sighed one man named Sergiy who said he had worked at the headquarters.

He denied Ukrainians were surrendering or switching sides, but said they felt betrayed.

"Those serving in Crimea have been betrayed by the admiral, the commanders in Kiev. We will wait for what they decide now. If the (new pro-Russian authorities) tell me to leave Crimea, I will leave. I am not a partisan," he said.

"The vote was a farce," he said of the Sunday referendum on the peninsula which overwhelmingly supported joining up with Russia.

No shots were fired by either side and the militants said they had captured the head of the Ukrainian navy, Sergiy Gayduk -- a report later confirmed by Ukraine's defence ministry.

"The military base is now under control. There was no use of guns," said Igor Yeskin, a representative of the pro-Moscow militants, referred to in Crimea as the "self-defence forces".

He said the aim was to overtake all Ukrainian military outposts without bloodshed. The servicemen had been told that if they resigned "they could stay in Sevastopol or they can leave the territory of Crimea".

If they stay in the military and want to stay "they can serve the people of Crimea or in the future they can join the Russian army," he said.

Yeskin gave few details about Gayduk's capture but said: "He was blocked and he had nowhere to go. He was forced out and he has been taken away."

Gayduk was only appointed this month after his predecessor, Rear Admiral Denis Berezovsky, deserted his post and pledged allegiance to the new pro-Moscow authorities in Crimea.

Asked why and where Gayduk had been taken, Yeskin said it had been in order "to have another conversation" with him.

"The authorities are dealing with this," he said.