The several hundred militiamen who captured the base in Sevastopol met no resistance. Sevastopol is also the home port of Russia's Black Sea Fleet, and tens of thousands of Russian-led troops are now patrolling Crimea.
It came a day after a confrontation between Ukrainian soldiers and pro-Russian militia left two dead.
The Russian-speaking troops, who arrived on the base after the storming, wore helmets, flak jackets and uniforms with no identifying insignia. By afternoon, they were in full control of the naval headquarters, a set of three-story boxy white concrete buildings with blue trim. It was not immediately clear how many, if any, Ukrainian servicemen remained on the base.
Ukraine's Defense Ministry said no one was injured in the raid, which it said was led by pro-Russian militiamen and Cossacks.
The ministry said in its statement that Rear Adm. Sergei Haiduk was detained by unknown people after the storming of the fleet headquarters. The Russian state ITAR-Tass news agency reported that he was being questioned by Crimean prosecutors.
Ukraine's defense minister and deputy prime minister had planned to travel to Crimea on Wednesday in what they said was a bid to avert an escalation in hostilities.
The prime minister in Crimea warned after the announcement of their departure that they would be turned back, however.
"They are not welcome in Crimea," Sergei Aksyonov was quoted as saying by the Interfax news agency. "They will not be allowed to enter Crimea. They will be sent back."
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.
Thousands of troops under apparent Russian command took over Crimea two weeks before Sunday's hastily called referendum, seizing Ukrainian military bases, blockading others and pressuring Ukrainian soldiers to surrender their arms and leave.
Putin insisted Russia's military presence in Crimea was limited to those stationed under the terms of a treaty with Ukraine that allows Russia to have up to 25,000 troops at its Black Sea fleet base. Ukraine claims that Russia deployed further forces, however, and expressly went against its request for troops to remain confined within their barracks.