Angry locals surrounded General Vasily Krutov, yelling questions about what he and his troops were doing in their city.

"We are conducting an anti-terrorist operation," the senior Ukrainian officer began, but he was interrupted by angry shouts of "What terrorists?"

As the crowd surged towards the airfield entrance in Kramatorsk in eastern Ukraine, waving a Russian flag on a long branch, the Ukrainian troops inside unleashed a volley of shots into the air.

After a failed ultimatum for pro-Russian protesters to lay down their arms and vacate government buildings they have occupied in at least nine cities across eastern Ukraine, yesterday Kiev attempted to flex its military muscle. But the anti-terrorist operation announced by the acting president, Oleksandr Turchynov, got off to a rough start when security service troops took control of the military facility, firing shots and injuring at least two protesters. The air base is an obvious staging point for any operation in the larger nearby city of Slavyansk, where well-organised gunmen seized the police and security service building last weekend. A similar group of armed men later stormed a government building in Kramatorsk with a flurry of gunfire, although no one was injured.

The casualties angered still further locals opposed to the Kiev government. Men quickly hemmed the troops inside the air base with tyres, pallets and small trees they had uprooted, vowing to guard the barricade through the night and set it on fire if anyone tried to come out. A few dozen molotov cocktails stood on the road nearby.

Although officials blame the unrest on Russian agents, including a man who identified himself on camera as a lieutenant general in the Russian army, local protesters say they are acting on their own initiative, out of their hatred for the new regime. The mayor of Slavyansk said on Ukrainian television on Tuesday that soldiers from Russia and Crimea had led the building takeovers there.

Speaking with Krutov, the crowd demanded to know why the troops, sent by Kiev to quell an uprising in eastern Ukraine that officials say Russia is inciting, had fired on locals, with one man displaying a wound on his thigh he said was from a bullet graze. The general said about 30 armed men were operating in the area and his men had been forced to open fire, but he was quickly drowned out by shouts and chants of "Lies!" and "Donbass!," the historical name of this coal-mining region with close economic and cultural ties to Russia.

At one point, a group of men began punching Krutov in the head, knocking off his military-issue fur hat. Yelling "jail him", they attempted to drag him away, but others stopped them and escorted him to the base's entrance.

A man who identified himself only as Sergei said he had been in the group of men that had come under fire at the airfield, saying two of them had been wounded. He said after they saw two helicopters land and unload special forces, he and a dozen or so others advanced on the base armed with clubs. After they passed through the gates, soldiers began shooting at them, he said, denying reports that men in the party were carrying firearms.

Arriving at the facility, the Guardian also saw a fighter jet resembling a Su-27 circling around the airfield. Locals claimed it had strafed the airfield earlier.

Speaking to journalists, Krutov said the wave of unrest was being led by Russian forces. He said more than 300 Russian forces had infiltrated neighbouring Luhansk region the day before.

"We need to destroy this foreign invader. We have among these spies Russian military, professionals with long experience in all sorts of conflicts."

Asked if another ultimatum would be given to those who had seized buildings, Krutov said that would be "too humanitarian". Civilian casualties were possible, but his forces would try to "make sure not one innocent person suffers".

"Unfortunately we face a difficult situation because those realising their plan are hiding behind human shields," he said, apparently referring to the many pro-Russian locals who have taken part in building takeovers.

"People don't want to turn in their weapons. As soldiers, we are obliged to defend our land," said a paratrooper with the anti-terrorist force who declined to give his name. "We believe in everything we're doing to preserve our government, our territory and peace here. No one is planning to fight with protesters."

"Some of them are cynically working towards their own ends, but many are under the influence of propaganda," Krutov said about the pro-Russian protesters. Russian media have painted the new Kiev government as dominated by nationalists who want to crack down on Russian speakers in the east.

"We're not separatists," a man who identified himself only as Valery said outside the barricaded airfield. "I don't want Ukraine to be divided. I don't want to give our land to Russia … I want a referendum because we can't work with this regime any other way."