The dramatic seizure came as Russia and the West dug in for a long confrontation over Moscow's annexation of Crimea, with the United States and Europe groping for ways to increase pressure on a defiant Russian President Vladimir Putin.
"As long as Russia continues on this dark path, they will face increasing political and economic isolation," said US Vice President Joe Biden, referring to reports of armed attacks against Ukrainian military personnel in Crimea.
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Biden was in the Lithuanian capital Vilnius, part of a quick trip to reassure Baltic allies worried about what an emboldened Russia might mean for their nations.
Lithuania, along with Estonia and Latvia, are NATO members.
"There is an attempt, using brutal force, to redraw borders of the European states and to destroy the post-war architecture of Europe," Lithuanian President Dalia Grybauskaite said.
United Nations chief Ban Ki-moon meets Putin in Moscow on Thursday and travels to Kiev on Friday. He will urge a peaceful end to a crisis that began when Ukraine's president abandoned a trade pact with the European Union and turned instead to Moscow, prompting violent street protests that led to his overthrow.
Russian lawmakers raced to ratify a treaty making Crimea part of Russia by the end of the week, despite threats of further sanctions from Washington and Brussels.
The Russian military moved swiftly to neutralise any threat of armed resistance in Crimea.
Read: Obama: Russia has violated international law in Ukraine
"This morning they stormed the compound. They cut the gates open, but I heard no shooting," said Oleksander Balanyuk, a captain in the navy, walking out of the compound in his uniform and carrying his belongings.
"This thing should have been solved politically. Now all I can do is stand here at the gate. There is nothing else I can do," he told Reuters, appearing ashamed and downcast.
Ukrainian military spokesman Vladislav Seleznyov said the commander of the Ukrainian navy, Admiral Serhiy Haiduk, was driven away by what appeared to be Russian special forces.
In Washington, the White House condemned Russian moves to seize Ukrainian military installations, saying they are creating a dangerous situation. NATO accused Russia of trying to "redraw the map of Europe".
Read: Putin has chosen path to Russia's isolation: Britain
Pro-Russian forces used a tractor to ram through the gate of a Ukrainian navy base in western Crimea on Wednesday, seizing control of the entrance, Ukraine's defence ministry said.
"Russian soldiers" then halted their advance, ministry spokesman Vladislav Seleznev said on his Facebook page, adding that they were now in a standoff with armed Ukrainian troops at the base in Novoozerne.
An Associated Press photographer witnessed several hundred self-defence forces take down the gate and make their way onto the headquarters' premises. They then raised the Russian flag on the square by the headquarters.
A Ukrainian soldier stands guard at a check point at the border between Ukraine and Crimea near the Salkovo village near Kherson. (AFP Photo)
Ukrainian servicemen were standing guard by the main building. Crimean self-defense forces are not armed and seemed to be waiting for the Ukrainian army's decision whether to let them in.
The commander of the Russian Black Sea fleet was seen arriving at the base for talks.
Russian President Vladimir Putin on Tuesday signed a treaty to incorporate Crimea into its territory following a referendum in which residents of Ukraine's region overwhelmingly backed the move. Jubilant crowds in Moscow and other cities across Russia hailed the annexation while Ukraine's new government called the Russian president a threat to the "civilized world and international security," and the US and Europe threatened tougher sanctions against Moscow.
A Ukrainian serviceman and a member of a local self-defense brigade were killed by gunfire in an incident in Crimea on Tuesday.
Watch: Putin signs treaty with Crimean leaders on Ukrainian Black Sea peninsula
Thousands of Russian troops had overtaken Crimea two weeks before Sunday's hastily called referendum, seizing some Ukrainian military bases, blockading others and pressuring Ukrainian soldiers to surrender their arms and leave. Putin insisted the Russian troops were in Crimea under a treaty with Ukraine that allows Russia to have up to 25,000 troops at its Black Sea fleet base in Crimea.
The West and Ukraine described the Crimean referendum as illegitimate and being held at gunpoint.
The United States and the European Union on Monday imposed sanctions on Russia, targeting Russian and Crimean officials with visa bans and asset freezes.
(With AP inputs)
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Welcome to Republic of Crimea, the world's newest statelet