The three pro-Russian separatists were killed in a clash with Ukrainian forces in Mariupol, Interior Minister Arsen Avakov said on Facebook.
The Geneva meeting is the first such gathering since the crisis escalated.
The West says Russia is aiding the pro-Russian activists occupying buildings.
In a live TV phone-in on Thursday Russia’s President Vladimir Putin warned Kiev of “the abyss they’re heading into” in eastern Ukraine and urged dialogue.
Vladimir Putin said the Kiev government, which had “seized power”, had only spoken to its own appointees in the region, but “not to the people whom locals trust”.
Tensions escalated last month when Russia annexed Crimea, causing international outrage. Unrest later spread to Donetsk region, another mainly Russian-speaking area. It is Europe’s worst crisis since the Cold War.
Vladimir Putin is now taking questions from residents of Sevastopol, base of the Russian fleet in Crimea, the first place to feature in his phone-in. It is the first time Crimea has been included in Vladimir Putin’s annual phone-in.
Overnight about 300 pro-Russian separatists attacked a military unit in Mariupol near the Azov Sea, throwing petrol bombs. Troops opened fire, killing three, Arsen Avakov said.
The operation is continuing – Ukraine has sent in reinforcements including helicopters. There was no independent confirmation of his statement.
According to Arsen Avakov, 13 of the attackers were wounded and so far 63 have been detained. He said none of the interior ministry troops had been killed.
It is the heaviest casualty toll in any single incident so far in eastern Ukraine.
Mariupol is in the far south of Donetsk region, where separatists have seized dozens of official buildings.
Ukrainian SBU special forces have gone to the aid of the interior ministry troops in Mariupol and armored vehicles have gone into the city from places nearby, Ukraine’s Unian news agency reports.
Retreating separatists reportedly wounded two passers-by, set a minibus ablaze and also set fire to a building next to the military garrison.
“Through joint efforts by the armed police and national guard the attacking gang was dispersed after a short battle, most of them were cornered and disarmed,” Arsen Avakov said.
“Because it was such an aggressive attack on a military unit – an interior ministry group – we decided to reinforce them with Omega special forces. Helicopters have been deployed.”
According to a report on Russia’s state-run Vesti TV news, unarmed local protesters tried to talk to the Ukrainian troops but were met with gunfire. Quoting unnamed Mariupol residents, the TV channel said shots were also fired at first-aid paramedics.
Some locals say Ukrainian Right Sector ultra-nationalists have joined Kiev’s forces in Mariupol, while separatists have erected street barricades, the TV reports.
Russia’s annexation of Crimea has fuelled concern that other parts of eastern Ukraine could also break away from Kiev’s control and join Russia.
In his TV broadcast, President Vladimir Putin said Russia had “never planned to annex Crimea or take military action there, but threats to Russian speakers there were real”.
He again denied allegations of Russian involvement in eastern Ukraine, calling them “nonsense”.
Earlier, President Barack Obama warned Russia against support for further action by armed pro-Russian groups.
“What I have said consistently is that each time Russia takes these kinds of steps that are designed to destabilize Ukraine and violate their sovereignty, that there are going to be consequences,” he said.
Reports say that the White House is considering a package of non-lethal aid for the Ukrainian military. This may include clothing and medical supplies.
Meanwhile, Ukraine’s military operation against separatists has hit obstacles.
Called an “anti-terrorist” operation by the Kiev government, it started on Tuesday and is designed to dislodge pro-Russia gunmen from local authority buildings in a swathe of cities and towns in eastern Ukraine.
Pro-Russian activists want referendums on greater autonomy for the south-east or the right to join the Russian Federation.
But in several districts, Ukrainian troops met vehement opposition on Wednesday from pro-Russia militants.
In the city of Kramatorsk, six military vehicles were commandeered by gunmen, who disarmed the Ukrainian soldiers and sent some of them home on buses.
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