Most of the men loyal to Jean-Pierre Bemba, who lost presidential polls last year, have fled the business district.
Eyewitnesses say dozens of bodies, riddled with bullet wounds, have been moved from the streets and civilians have been ordered to stay indoors.
Earlier, an arrest warrant was issued for Mr Bemba on grounds of treason.
He has taken refuge in the South African embassy compound and has denied plotting military action to overthrow President Joseph Kabila.
A deadline for Mr Bemba's guards to disarm expired this week but he wants additional security guarantees before they lay down their weapons.
Last year's election - the first free poll in four decades - passed off peacefully, raising hopes of an end to years of conflict and mismanagement.
Looting
The BBC's Arnaud Zajtman in Kinshasa says sporadic shooting can still be heard but government soldiers have taken control of the city's business centre.
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They have used plastic chairs and bricks to set up roadblocks in the capital.
Several supermarkets, shops and private houses have also been looted by the government troops, our reporter says.
Mr Bemba's guards have been seen running away, abandoning their uniforms and surrendering to UN peacekeepers.
A doctor in charge at Kinshasa's hospital told the BBC that 32 people were being treated for gunshots wounds.
Other sources report 60 bodies have been brought to the hospital, which tallies with eyewitness accounts, our correspondent says.
'Life in danger'
Mr Bemba has immunity as a senator but the government says this may be stripped.
South Africa's deputy Foreign Minister Aziz Pahad urged all sides to stop fighting but did not say whether the former rebel leader would be handed over to the Congolese authorities.
"Bemba committed treason in using the armed forces for his own ends," said Congolese government spokesman Toussaint Tshilombo.
But Mr Bemba denied trying to oust Mr Kabila and said his house had been attacked four times.
"I feel they want to kill me," he told the BBC. He has called for negotiations with the government about his security arrangements.
As a former vice-president in the transitional government, he is entitled to 15 policemen for his protection.
Under another agreement signed ahead of the election, the winner of the presidential poll is committed to guarantee the loser's security.
But the country's information minister said that since the government was democratically elected last year, there was no reason for fresh talks.
President Joseph Kabila won 58% of the vote compared to Mr Bemba's 42% in an election run-off last October.
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