"I am appealing to the military leadership of the Russian Black Sea fleet," said Olexander Turchinov, acting president since the removal of Yanukovich last week. "Any military movements, the more so if they are with weapons, beyond the boundaries of this territory [the base] will be seen by us as military aggression.
Ukraine's Foreign Ministry also summoned Russia's acting envoy in Kyiv for immediate consultations.
There were mixed signals from Moscow, which put fighter jets along its western borders on combat alert, but earlier said it would take part in discussions on an International Monetary Fund (IMF) financial package for Ukraine. Ukraine has said it needs $35 billion US over the next two years to stave off bankruptcy.
The fear of military escalation prompted expressions of concern from the West, with NATO Secretary-General Anders Fogh Rasmussen urging Russia not to do anything that would "escalate tension or create misunderstanding".
Polish foreign minister Radoslaw Sikorski called the seizure of government buildings in the Crimea a "very dangerous game".
It was not immediately known who was occupying the buildings in the regional capital Simferopol and they issued no demands, but witnesses said they spoke Russian and appeared to be ethnic Russian separatists.