Shots were fired, a grenade thrown and 70 people detained as officers ended the occupation in the city of Kharkiv during an 18 minute "anti-terrorism" action, said the interior ministry.
But elsewhere in Ukraine's mainly Russian-speaking industrial heartland, activists armed with Kalashnikov rifles and protected by barbed wire barricades promised there was no going back on their demand - a vote on returning to Moscow rule.
In the city of Luhansk, a man dressed in camouflage told a crowd outside an occupied state security building: "We want a referendum on the status of Luhansk and we want Russian returned as an official language."
"We will not let fascism pass," he shouted, leading the crowd in chants of "Russia! Russia!".
Ukraine says the seizure of public buildings in eastern regions on Sunday night is a replay of events in Crimea, the Black Sea peninsula Moscow annexed last month after a referendum staged when Russian troops were already in control.
In Kiev, Interior Minister Arsen Avakov partly pinned responsibility for the Kharkiv occupation on Russian President Vladimir Putin. "All this was inspired and financed by the Putin-Yanukovich group," he said.
An aide said police went in when the protesters failed to give themselves up and surrender their arms. Officers did not open fire, despite shooting and the grenade attack from the other side, he said. One officer was badly wounded and some others less seriously hurt.
In Luhansk, a city of about 450,000 people, protesters blocked streets leading to the state security building with barbed wire, piles of tyres, wooden crates, metal police barriers and sandbags. Protesters at the entrance to the building blocked the entrance with metal shields.
One man, who said he had stormed the building on Sunday, said the protesters had 200-300 Kalashnikovs and some stun grenades, but there had been no shooting so far. He said: "I'll stay here until the end, until victory. Once you've taken up arms, there is no turning back. We will stay until the authorities agree to hold a referendum on the status of Luhansk."
He said he had sent his family to Russia after Moscow-backed president Viktor Yanukovich fled after being overthrown in February. "They couldn't stay here. I knew what would happen after the bandits took over, I knew it would only lead to war. And war is what we're getting," he said.
A standoff also continued in the mining centre of Donetsk, Mr Yanukovich's home base, where a group of pro-Russian deputies inside the main regional authority building on Monday declared a separatist republic.
Unlike in Kharkiv, there was no clear sign further police operations were imminent in the other two cities. "We hope the buildings occupied in Donetsk and Luhansk will soon be freed," said acting president Oleksander Turchinov.
Russia has warned Kiev against using force to end the occupations but authorities may anyway have decided not to give Moscow an excuse to intervene, holding back in the hope the protests will fizzle out.
Russian Foreign Minister Sergei Lavrov dismissed Western accusations Moscow was destabilising Ukraine, saying the situation could improve only if Kiev took into account the interests of Russian-speaking regions.
But Britain expressed fears Russia wanted to disrupt the run-up to presidential elections next month in Ukraine, which has been ruled by an interim government since the overthrow of Mr Yanukovich.
Ukraine, which was controlled by Moscow until the Soviet Union collapsed in 1991, has been in turmoil since late last year when Mr Yanukovich rejected closer relations with the European Union and tilted the country back towards Russia. That provoked mass protests in which more than 100 people were killed by police and which drove Mr Yanukovich from office, leading to Kiev's loss of control in Crimea.