The moves pose an immediate challenge to Ukraine's new authorities as they sought to set up an interim government for the country, whose population is divided in loyalties between Russia and the West.
Some 150,000 Russian soldiers carried out military exercises and fighter jets patrolled the border.
A respected Russian news organisation, meanwhile, reported that President Viktor Yanukovych, who was driven out of Kiev by a three-month protest movement, was staying in a Kremlin sanatorium just outside Moscow.
Shortly after, the same three Russian news agencies quoted an unnamed Russian official saying that Yanukovych's request for protection "was satisfied on the territory of Russia."
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Oleksandr Turchynov, who stepped in as acting president after Yanukovych's flight, condemned the takeover of government buildings in Crimea as a "crime against the government of Ukraine." He warned that any move by Russian troops off of their base in Crimea "will be considered a military aggression."
"Unidentified people with automatic weapons, explosives and grenades have taken over the governmental buildings and the Parliament building in the autonomous region of Crimea," he said.
In Kiev, lawmakers were expected to approve the new government that will face the hugely complicated task of restoring stability in a country that is not only deeply divided politically but on the verge of financial collapse.