By Aleksandar Vasovic and Gabriela Baczynska

SEVASTOPOL/SIMFEROPOL, Ukraine (Reuters) - Russian troops and unarmed men stormed Ukraine's naval headquarters in the Crimean port of Sevastopol on Wednesday and raised the Russian flag in a tense but peaceful takeover that signals Moscow's intent to neutralize any armed opposition.

Russian soldiers, and so-called "self-defense" units of mainly unarmed volunteers who are supporting them across the Black Sea peninsula, moved in early in the morning and quickly took control.

Shortly after the incident, Ukraine's acting Defence Minister Ihor Tenyukh said in Kiev that the country's forces would not withdraw from Crimea even though Russian President Vladimir Putin has signed a treaty to make it part of Russia.

But an hour later, Ukrainian servicemen, unarmed and in civilian clothing, began walking out of the headquarters.

Interfax Ukraine news agency said the commander of the Ukrainian navy, Admiral Serhiy Haiduk, was among those who left and was driven away by officers of Russia's FSB intelligence service. The report could not be independently confirmed.

The first group of servicemen was followed within a few minutes by a handful of troops in Ukrainian uniform, looking shell-shocked at the dramatic turn of events.

"This morning they stormed the compound. They cut the gates open, but I heard no shooting," said Oleksander Balanyuk, a captain in the navy.

"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.

Russia's Itar-Tass news agency reported that Alexander Vitko, commander of Russia's Black Sea Fleet which is based in Sevastopol, had been involved in talks at the headquarters.

Viktor Melnikov, in charge of the "self-defence" unit, said talks were going on to negotiate a surrender.

"We've had difficult negotiations with the command here," he told reporters. "Some Ukrainian servicemen are already leaving, without their uniforms, but there was no violence."

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A Reuters reporter saw three armed men, possibly Russian soldiers in unmarked uniforms, at the gate and at least a dozen more inside the compound.

PROTECTION FROM "FASCISTS"

In Kiev, pro-Western Ukrainian Prime Minister Arseniy Yatsenyuk ordered his first deputy prime minister and the acting defence minister to fly to Crimea to "resolve the situation," a senior minister told a cabinet meeting.

But Sergei Askyonov, Crimea's new prime minister since the Russian takeover, said Vitaly Yarema and Ihor Tenyukh were not wanted in Crimea and would not be permitted to land.

Thousands of Russian soldiers took control of Crimea in the buildup to a weekend referendum last weekend in which the region, with ethnic Russians in the majority, voted overwhelmingly to leave Ukraine and join Moscow.

Putin said his move to take control of Crimea was justified by what he calls "fascists" in Kiev who overthrew pro-Moscow president Viktor Yanukovich last month after three months of often deadly street protests.

Ukraine and Western governments have dismissed the referendum, which has triggered the worst crisis in East-West relations since the Cold War, as a sham, and say there is no justification for Putin's actions.

Moscow officially denies deploying extra troops and Russian soldiers in the region are wearing unmarked uniforms, making it difficult to verify exactly who is who on the ground.

In Crimea's main city, Simferopol, where one Ukrainian serviceman was killed after a shooting on Tuesday, the situation was calm on Wednesday.

It was the first death on the Black Sea peninsula from a military clash since the region came under Russian control three weeks ago. Ukrainian prime minister Yatseniuk denounced it as a "war crime".

Aksyonov, Crimea's pro-Moscow leader, suggested the incident was the fault of "provocateurs" opposed to the annexation of the region to Russia.

"Unfortunately, two people were killed," he said, speaking in Moscow. "I'm sure we will find these scoundrels. The security service of the Crimean Republic is investigating."

(Additional reporting by Mike Collett-White in Simferopol and Steve Gutterman in Moscow; Writing by Mike Collett-White; Editing by Ron Popeski)