At least three people died in the raid on a checkpoint manned by pro-Russian separatists near the town of Sloviansk.
Russia expressed “outrage” at the shooting and said Ukraine’s Right Sector nationalists were to blame.
The incident came as pro-Russian groups continued to occupy government buildings defying a deal to leave.
The deputy secretary of Ukraine’s national security council, Viktoriya Siumar told the BBC that it was too early to tell who was responsible for the attack.
Criminal groups could have been behind the incident, she said, adding that “the level of criminality in eastern Ukraine has increased substantially recently”.
Ms Siumar said that Kiev was “concerned” about the fact that Russia had already reached its own conclusions.
Russian television showed an interview with a man, allegedly captured after the attack, who said he was a Right Sector member.
However, a spokesman for the group denied that the man was a member.
“Right Sector was not there, and whatever happened there was an obvious provocation from the Russian secret services,” Artyom Skoropadskiy said.
The Right Sector mocked the discovery of a business card found in a burned out car at the site and said to belong to its leader Dmytro Yarosh.
Mr Skoropadskiy said this was “propaganda worse than that of Nazi Germany”, adding: “As if the militants of Pravy Sektor carry Yarosh’s business cards with them!”
The Russian foreign ministry accused the Kiev government of not doing enough to protect Russian speakers.
“Russia is indignant about this provocation by gunmen, which testifies to the lack of will on the part of the Kiev authorities to rein in and disarm nationalists and extremists,” it said in a statement.
Russia, Ukraine, the EU and US agreed during talks in Geneva last Thursday that illegal military groups in Ukraine must be dissolved, and that those occupying government premises must be disarmed and leave.
But the separatists’ spokesman in the city of Donetsk said that the Kiev government was “illegal”, and vowed they would not go until it stepped down.
The shooting is the first fatal incident in the region since Thursday’s agreement.
Sloviansk rebel leader and self-proclaimed mayor Vyacheslav Ponomarev called on Russian President Vladimir Putin to send peacekeepers to the region. He also asked for food and weapons.
Mr Ponomarev added that a “people’s army of Donbass” was being set up. Donbass (Don river basin) is the industrial area of eastern Ukraine made up of Donetsk and Luhansk regions.
The BBC’s James Reynolds in Donetsk says that the Geneva deal is already in trouble and events in Sloviansk will do little to change that.
Meanwhile, Ukraine’s navy said that seven of its ships that were stationed in Crimea – now annexed by Russia – had returned to the port of Odessa.
However, the captain of the Kirovograd said that his crew had decided to join the Russian armed forces.
“The ship has been operating for 11 years, unfortunately its crew decided to stay in Russia, but they have saved this ship and I am grateful for this,” said Dmitry Kovalenko.
US Vice-President Joe Biden is set to meet Ukraine’s acting president and prime minister on Tuesday on a two-day visit to Kiev.
Ukraine’s interim Prime Minister Arseniy Yatsenyuk criticised Russia’s Vladimir Putin in a US TV interview ahead of the visit.
He told NBC’s Meet the Press programme that Mr Putin had a “dream to restore the Soviet Union”.
“It’s crystal clear that for today, Russia is the threat to the globe, and the threat to the European Union, and a real threat to Ukraine,” Mr Yatsenyuk said.
Ukraine has been in crisis since President Viktor Yanukovych was toppled in February.
Russia then annexed Crimea following a regional referendum that approved joining the Russian federation. The annexation provoked international outrage.
Pro-Russian activists then occupied buildings in several eastern Ukrainian cities.
Ukraine has said that operations against the pro-Russian militants have been suspended over Easter.
Ukraine’s interim authorities have appealed for national unity and promised to meet some of the demands of pro-Russian protesters.
These include the decentralisation of power and guarantees for the status of the Russian language.
But the US has warned the next few days will be pivotal and has threatened more sanctions against Russia if it fails to abide by the agreement.