Interfax later cited Welfare Minister Lyudmila Denisova as saying the officials had been denied entry to Crimea. She said an emergency session of the National Security and Defense Council will held in response.
At the Ukrainian navy headquarters, an Associated Press photographer said the militiamen took down the gate and made their way onto the base. They then raised the Russian flag on the square by the headquarters.
The unarmed militiamen waited for an hour on the square and, following the arrival of the commander of the Russian Black Sea Fleet, they took over the building.
The AP photographer was able to enter the headquarters and saw the militia roaming around while the Ukrainian servicemen were packing up and leaving.
On Tuesday, President Vladimir Putin signed a treaty to incorporate Crimea into Russia following a referendum Sunday in which residents of the region overwhelmingly backed the move.
Jubilant crowds in Moscow and other cities across Russia hailed the annexation, while Ukraine's new government called Putin a threat to the "civilized world and international security," and the U.S. and the European Union threatened tougher sanctions against Moscow. On Monday, Washington and Brussels targeted Russian and Crimean officials with visa bans and asset freezes.
Russian news agencies on Wednesday cited Constitutional Court chairman Valery Zorkin as saying the treaty signed by Putin has been ruled valid, thus formally clearing another hurdle for Moscow to annex Crimea. The treaty now only requires ratification by the Russian parliament.
A Ukrainian serviceman and a member of a militia were killed by gunfire in the incident in Crimea on Tuesday.
It is unclear whether the militiaman was a Ukrainian citizen. Although Moscow has insistently denied it has not deployed its own troops in Crimea, people in the peninsula have reported seeing a large number of military vehicles with Russian plates.