An armoured vehicle also smashed open the front gate of the Belbek base near the port city of Sevastopol, said the Ukrainian defence ministry.
Two ambulances arrived and then departed shortly after. At least one appeared to be carrying a wounded person.
Yuliy Mamchur, the Ukrainian commander of the base, said he had called his men together, who sang the Ukrainian anthem and then stood at ease. He said they would turn over their weapons.
Russian forces have been occupying Ukrainian military facilities for several days in the Black Sea peninsula, which voted in a referendum a week ago to join Russia.
The takeover has been largely bloodless, though one Ukrainian serviceman was killed and two others wounded in a shooting in the regional capital, Simferopol, last week. A Russian Cossack militiaman was also killed. Yesterday both men were buried after a joint funeral service in Simferopol.
Ukraine’s defence ministry said on Friday that Crimea’s bases were still formally under its control, but most were now occupied by Russian troops and fly Russia’s tricolour flag.
In other developments yesterday Ukrainian police seized 42 kilograms of gold and $4.8 million (£2.9m) in cash from the home of the former energy minister Eduard Stavytsky during a corruption investigation. New interior minister Arsen Avakov said: “It blew my mind when I received a report on the results. How much would one have to steal to have such a ‘trifle’ at home as pocket money.”
Stavytsky’s career blossomed under the presidency of Viktor Yanukovich and he was appointed energy minister in December 2012.
It is not clear how he could have amassed such a fortune.
Yanukovich himself collected just $25,000 (£15,000) a year in pay, though he lived on a country estate estimated by some reports to be worth around $75m.
In the eastern Ukrainian city of Donetsk yesterday, more than 5,000 pro-Russia residents waving Russian flags demonstrated to call for a referendum on whether to seek to split off and become part of Russia. They were confronted by lines of shield-wielding riot police around the regional administrative headquarters.
Inside, German foreign minister Frank-Walter Steinmeier was meeting local officials.
The demonstrators erected several tents at the site.
“I’m ready to live in a tent, but I’m not ready to submit to the West, to dance to their tune,” said Viktor Rudko, a 43-year-old miner.
The rally came less than a week after Crimea approved secession. Concern is now rising that Ukraine’s eastern regions will agitate for a similar move. Russia has brought large military contingents to areas near the border with eastern Ukraine.
President Vladimir Putin has said there is no intention to move into eastern Ukraine, but the prospect of violence between pro-and anti-secession groups in the east could be used as a pretext for military intervention.
Eastern Ukraine is the heartland of Ukraine’s heavy industry and mining and the foundation of Yanukovich’s past electoral popularity.
As tensions grow in the east, the Organisation for Security and Co-operation in Europe, with Russian agreement, is deploying a 200-strong observer team aimed at easing the crisis.
The seizure of military facilities and navy ships by pro-Russian forces in Crimea has been proceeding apace since the peninsula was last week nominally absorbed by Russia.
Yesterday, a crowd also stormed the Novofedorivka base, some 50 kilometres west of Simferopol, Ukraine’s defence ministry said.
Ukrainian television said troops inside the base lobbed smoke grenades in an attempt to disperse gangs of young men attempting to break through the front gates.
On Friday, Russia said fewer than 2,000 of 18,000 Ukrainian servicemen in Crimea had “expressed a desire to leave for Ukraine”.