Ukrainian military orders troops to protect themselves after soldier was killed in military base near Simferopol

Ukraine has ordered its troops in Crimea to use their weapons to protect themselves after a soldier was killed when pro-Russian forces stormed a military base near Simferopol – the first military casualty since the peninsula was occupied by Russian forces three weeks ago.

"The conflict is shifting from a political to a military stage," said Ukraine's interim prime minister, Arseniy Yatsenyuk, at an emergency government meeting on Tuesday night. "Russian soldiers have started shooting at Ukrainian military servicemen, and that is a war crime." Moscow has not yet responded.

A Ukrainian military spokesman, Vladislav Seleznyov, said that one soldier had died and another was injured after they were shot when the base was attacked by "unknown forces, fully equipped and their faces covered". It was unclear whether the assailants were Russian troops or pro-Moscow militiamen, who have been active in their support for Crimea's occupation.

Hundreds of Ukrainian troops and administrative staff remained trapped inside military and naval compounds across Crimea. Until now they had been ordered to avoid using their weapons.

Earlier this week the Russian defence ministry reportedly told Ukrainian soldiers they had until Friday to leave the region or face military action. Meanwhile, a deal was reportedly reached between Russian and Ukrainian commanders to allow supplies and people to enter and exit the bases more freely.

But on the ground, tensions appear to have risen in the last few days.

At the entrance to Bakhchysarai military base, the Ukrainian army's insignia had been removed and replaced with a pair of large Russian flags. Just inside the gates, three men in military fatigues – two of them wearing Russian army uniform with no markings – raised their weapons as journalists approached, and threatened to open fire.

Speaking by telephone from inside, Aleksandr Krotov, a captain in Ukraine's naval fleet, said the base was now mostly in the hands of Crimean irregulars and Russian troops, but he and fourteen other officers had been holed up in their offices for 19 days.

"If we leave we cannot go back inside," he said. "This is very clear." Krotov said he and his colleagues, who are guarding Ukrainian military vehicles inside the compound, had been subject to psychological intimidation and threats of physical harm by the forces occupying the base.

"We are only able to go the toilet under armed guard, and we have been threatened with being beaten and killed," Krotov added.

Outside, a small group of Ukrainian soldiers loitered nearby, listening to music in their cars and smoking cigarettes. One of them, who said his name was Yura, said they had been barred from entering since 1 March.

"We are here to support our guys inside," he said. "But if we try to approach the base [the pro-Russian forces] say they will shoot us. Kiev can only offer moral support in this situation, we don't know what will happen next".

Most local soldiers in their unit defected to the new Crimean army last week, which will soon be part of the Russian army. "They threatened to beat us to death if we did not surrender," said Yura.

Outside the base, Nina, the mother of one of the soldiers delivered food to the gate. "We are all very worried about everyone inside, and what could happen," she said.

Evgeniy Cherednichenko, head of armoured service at the logistical command centre in Sevastopol, told a similar story. Speaking by telephone, he said that Russian troops had blocked 50 army officers and 10 administrative personnel from leaving the base since Tuesday morning. "If we try to leave they threaten us with guns, they tell us not to approach the gate," he said.

Cherednichenko, who is from Sevastopol, said that those trapped inside were awaiting commands from Kiev about how to evacuate the base. "We are very anxious of what could happen in these next few days," he said.

Earlier, as news came in that Vladimir Putin had signed a draft bill to annex Crimea, cheers broke out among the armed men blockading another base near Simferopol.

"You are here for a historic moment, we have returned home," said Vladimir Ishmahov, a retired Ukrainian army colonel.

Pro-Moscow militiamen clapped and shook hands with Russian soldiers, while inside the besieged Ukrainian troops, who appeared unable to leave, could only look on as their captors celebrated.