Two trucks from Russia’s Black Sea Fleet outside the gates, surrounded by armed men.
No shots are believed to have been fired, and the assailants and trucks reportedly left after “negotiations”.
Troops wearing Russian uniform without insignia have blockaded bases since taking control of Crimea last week.
Some military installations and other buildings in the peninsula have been taken over, but both sides have so far held their fire.
On Friday evening, the Interfax-Ukraine news agency reported that about 100 Ukrainian personnel were stationed at missile defense base A2355.
Citing a duty officer and Ukraine’s defense ministry, the agency said a truck had rammed open the gates of the facility and about 20 “attackers” had entered, throwing stun grenades.
The Ukrainian troops immediately barricaded themselves inside a building and their commander began negotiations before any shots were fired, it added.
There were two military trucks with Russian number plates outside the gates, surrounded by irregular soldiers and a very hostile crowd of pro-Russian demonstrators.
Two journalists who attempted to take photographs were beaten badly.
Later, a Ukrainian officer told a Daily Telegraph journalist that the stand-off had ended after the “talks”, and that the Russian trucks and about 30 to 60 Russians troops had withdrawn.
The incident comes hours after Russian parliamentarians gave a standing ovation to a delegation of pro-Moscow politicians from Crimea, promising support if they wanted to become part of Russia.
The region is due to hold a referendum on March 16, on whether to join Russia or remain part of Ukraine. The vote has been denounced by the interim government in Kiev as illegitimate.
Meanwhile, Russia’s state-owned energy company, Gazprom, warned Ukraine that its gas supply might be cut off unless its $1.89 billion of debts were cleared.
Gazprom halted supplies to Ukraine for almost two weeks in 2009, a move that caused shortages in Europe.
Ukrainian officials have said the state has come close to bankruptcy since protesters ousted President Viktor Yanukovych at the end of February.
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