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"Armed lawbreakers and saboteurs who are terrorising the local population around Slaviansk... have turned to cynical provocation," the SBU security service said in a statement, describing the incident as a "staged attack".
No group was present "other than the saboteurs and crime figures, supported and armed by officers of Russia's GRU" military intelligence, the SBU added.
The Ukrainian nationalist group Right Sector, blamed by separatists for the shooting, denied involvement and also accused Russian special forces.
Russia has accused Ukraine of failing to protect civilians in the Russian-speaking east and has threatened to intervene on their behalf - as it did before annexing Crimea last month.
The Ukrainian interior ministry noted that its police were unable to operate in Slaviansk since pro-Moscow gunmen took over the town earlier this month.
But in a statement it said it had established that at least three men were killed in what it suspected might have been an incident set up by Russian agents.
Separatists manning a checkpoint on a road into Slaviansk near the town of Bylbasovka returned fire, it said, after gunmen in four cars drove up and shot at them at 02:20.
Three separatists were killed, two locals and a third as yet unidentified. Three were wounded. About a dozen attackers took off in two cars, carrying an unknown number of dead and wounded.
The interior ministry said none of its forces had mounted an operation overnight around Slaviansk, which it described as "the most dangerous place in Ukraine, in view of the presence in the town of foreign saboteurs and illegal armed groups".
"At the same time," it added, "One cannot but suspect the speed with which camera crews from Russian TV stations appeared at the scene of the shooting, and the obviously staged subject matter of news reports in the Russian media."
It noted that the news was broken by media run by Dmitry Kiselyov, a journalist who is close to Russian President Vladimir Putin and who, the ministry noted, is the subject of visa bans imposed by the US and EU as part of sanctions aimed at punishing Russia for annexing Crimea.
