The Interior Ministry said a mob of around 300 people armed with stun grenades and firebombs were involved in the bloodiest episode to date in the confrontation pitting Ukraine's new government in Kiev against an eastern insurgency tacitly supported by Moscow.
Masked and battle-ready militia bearing sophisticated firearms have been deeply involved in seizing government offices in eastern Ukraine, igniting suspicions that much of the unrest is being stirred with Russia's backing.
But Russia's President Vladimir Putin on Thursday dismissed as ''nonsense'' claims that Russian special forces were fomenting unrest in eastern Ukraine.
''It's all nonsense, there are no special units, special forces or instructors there,'' Putin said.
He did admit - for the first time - that the troops in unmarked uniforms who had captured Ukraine's Crimean Peninsula before its annexation last month by Moscow were Russian soldiers.
Putin also expressed hope that four-way talks between Ukraine, the U.S., the European Union and Russia in Geneva on Thursday could map a way out of the deepening security crisis.
Ukraine's interior ministry said shots fired by servicemen in the Mariupol base initially proved insufficient to deter the pro-Russian crowd from proceeding with their assault. It remains unclear exactly how the three protesters were killed.
There were no casualties among Ukrainian servicemen, the ministry said. At least 63 people involved in the attack were detained, but local media Thursday morning cited police as saying 38 were later released.
Speaking in parliament, acting President Oleksandr Turchynov said a pro-Russian gang carrying automatic weapons attempted to storm the base three times.
APTN footage filmed outside the base on Wednesday night showed an unidentified man acting as an intermediary coming out to speak to masked men in the crowd armed with assault rifles. He told them the military had asked for 10 minutes to think over an unspecified ultimatum.
The masked men insisted they wanted no bloodshed. A short while later, however, a crowd of mainly masked young men armed with bats and sticks began throwing Molotov cocktails at the base's gate and at the trucks parked in front of it. Sounds of gunfire were heard in response.
The skirmish came after the government announced an operation to retake control of the eastern city of Slovyansk, which has emerged as the focal point of the armed insurgency, and government buildings in several other cities in the east.
With tens of thousands of Russian troops deployed just across the border from Ukraine, there are fears the Kremlin might use the instability in the predominantly Russian-speaking region as a pretext for seizing more territory beyond its annexation of Crimea last month.
On Wednesday, hundreds of people in Kramatorsk, 15 kilometers (9 miles) south of Slovyansk, encircled a column of Ukrainian armored vehicles carrying several dozen troops. Soon after, masked gunmen in combat gear reached the site and Ukrainian soldiers surrendered the vehicles to them.
At another location near Kramatorsk, troops at 15 Ukrainian armored vehicles were also surrounded by a crowd. To end the standoff, Ukrainian servicemen handed over the magazines from their assault rifles to pro-Russian militia. The Defense Ministry said the infantry vehicles had left the area Thursday and were returning to their base in Dnipropetrovsk, 225 kilometers (140 miles) away.
There appeared little immediate sign of any planned military action by Ukraine forces. In an attempt to contain pro-Russian insurgents, a military checkpoint made of sandbags was built on the northern road to Slovyansk. An Associated Press reporter spotted 30 special forces officers, an armored personnel carrier and military vehicle with an anti-aircraft gun at the site.
Turchynov told parliament on Thursday that the brigade that handed over its vehicles would be disbanded and its members put on trial.
As the new government in Kiev struggles to contain the pro-Russian uprising, the Obama administration has said it is readying additional sanctions against Moscow and a boost in aid for the Ukrainian military in the coming days.