The dramatic escalation to the raging security crisis on the EU's eastern frontier came hours after President Vladimir Putin signed a treaty claiming Crimea as Russian territory after the Black Sea region overwhelmingly voted on Sunday in favour of switching from Ukrainian to Kremlin rule.
Ukraine's Western-backed Prime Minister Arseniy Yatsenyuk told an urgent government meeting in Kiev that his ex-Soviet country's conflict with its giant nuclear-armed neighbour was threatening to spiral out of control.
"Russian soldiers have started shooting at Ukrainian military servicemen, and that is a war crime," Yatsenyuk said.
Ukraine's interim president Oleksandr Turchnynov later issued a statement placing responsiblity for "the blood of Ukrainian soldiers (on) the leadership of the Russian Federation and specifically President Putin."
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Regional defence ministry spokesman Vladislav Seleznyov told AFP the soldier had died after being shot in the neck when a group of gunmen stormed a Ukrainian military base in the northeast of Crimea's main city of Simferopol.
But the Ukrainian defence ministry said in a statement the military base was attacked by people "dressed in the military uniforms of servicemen of the armed forces of the Russian Federation."
"For their self defence and protection of their lives, Ukrainian servicemen... Deployed in the Autonomous Republic of Crimea are allowed to use arms," the defence ministry said.
Ukrainian authorities had previously forbidden its Crimean soldiers from opening fire -- in some cases forcing them to stand guard at their bases with empty rifles -- in order not to proke a Russian offensive that could spill into an all-out war.
There was no immediate reaction to the reported death from either Russian authorities in Moscow or the peninsula's rebel leadership.