A Ukrainian serviceman was killed and another was injured at a military base that came under attack in Crimea's main city Simferopol.
Ukraine military spokesman Vladislav Seleznyov said it was unclear who had staged the assault, but described the attackers as "unknown forces, fully equipped and their faces covered".
It is believed to be the first death on the peninsula from a military clash since the region came under Russian control three weeks ago.
Earlier an unnamed Ukraine military spokesman claimed the raid was undertaken by Russian forces, telling the Interfax news agency, "They want us to put down our arms but we do not intend to surrender".
As news spread of the serviceman's death, Ukraine's acting president Oleksandr Turchynov said Russia was annexing Crimea in actions reminiscent of Nazi Germany's takeover of Austria in the run-up to World War II.
Interim Prime Minister Arseniy Yatsenyuk said the conflict had entered a military phase and accused Russia of committing "a war crime" over claims its forces had fired on Ukrainian servicemen.
Yatsenyuk said he had ordered Ukraine's defence minister to call a meeting with his counterparts from Britain, France, and Russia - signatories to a 1994 treaty guaranteeing Ukraine's borders to "prevent an escalation of the conflict".
The comments came after Russian President Vladimir Putin signed a treaty making Crimea part of Russia.
In a fiercely patriotic address to a joint session of parliament in the Kremlin, punctuated by standing ovations, cheers and tears, Putin said Crimea's disputed referendum vote had shown the overwhelming will of the people to be reunited with Russia.
As the Russian national anthem played, Putin and Crimean leaders signed the treaty, declaring, "In the hearts and minds of people, Crimea has always been and remains an inseparable part of Russia."
Putin later told the "We are Together" rally in Moscow's Red Square that Crimea had returned to "home port".
Foreign Secretary William Hague announced the Government had suspended military co-operation with Russia in light of the move, telling MPs the Ukraine crisis was the "most serious test of European security in the 21st Century so far"
The White House also condemned Putin's attempt to formally annex Ukraine's Crimea region, calling it "a threat to international peace and security" and "against international law".
In the city of Simferopol, hundreds of mourners gathered for the funeral of Reshat Ametov, a Crimean Tatar who was in his 30s.
Ametov reportedly disappeared on March 3 when three men in military jackets led him away from the scene of a protest in the city.
His body was found nearly two weeks later near the town of Belogorsk, (31 miles) 50 km east of Simferopol, showing signs of torture and beating.