At least 157 people were killed when Guinean troops opened fire on opposition protesters on Monday, a human rights group says.
But the country's interior ministry has told the BBC that a total of 57 people have died in the protests.
Human rights groups say they have had reports of soldiers bayoneting people and women being stripped and raped in the streets during the protest.
Junta head Capt Moussa Dadis Camara denied knowledge of sexual assaults.
But he admitted that some of his security forces had lost control.
French Foreign Minister Bernard Kouchner said France was suspending military ties with Guinea after the "savage and bloody" crackdown on opposition protesters, French news agency AFP reported.
Out of control
About 50,000 people were protesting over rumours that Capt Camara intends to run for president in an election scheduled for next January.
But soldiers moved in to quell the rally using tear gas and baton charges and firing live ammunition into the crowds.
The Guinean Organisation for Defence of Human Rights put the toll at 157 people killed and more than 1,200 wounded.
But the interior ministry told the BBC that a total of 57 people died during the violence.
The ministry source admitted that some soldiers had fired live rounds into the crowd, but said that only four people had died from gunshot wounds. The others, the ministry said, were trampled to death.
The opposition has accused the army of taking away some bodies to hide the scale of the violence.
Human rights groups said there were widespread reports of rape.
"The military is going into districts, looting goods and raping women," Mamadi Kaba, the head of the Guinean branch of the African Encounter for the Defence of Human Rights (RADDHO), told AFP.
"We have similar reports from several sources, including police sources and some close to the military," said Mr Kaba, from his office in Dakar, Senegal.
An eyewitness told Human Rights Watch: "I saw several women stripped and then put inside the military trucks and taken away. I don't know what happened to them."
"They were raping women publicly," opposition activist Mouctar Diallon said in an interview with French radio station RFI.
Guinean human rights activist Souleymane Bah told Reuters news agency that people trying to escape from the shooting were "caught and finished off with bayonets".
A doctor at a government hospital in Conakry said his wards looked like "a butchery".
Threat of sanctions
The BBC's Alhassan Sillah, in Conakry, says Capt Camara acknowledged that "uncontrollable soldiers" were responsible.
He told local radio stations that it was difficult to control the soldiers when there was tension in the country. The military strongman also said he was "immensely saddened" by the deaths.
Opposition leader Sidya Toure, who was arrested during the protests, told our correspondent that after his release he had returned home to find his home completely looted.
Mr Toure said he had witnessed women being sexually attacked with gun butts and added: "I don't know whether I'm on earth or in hell".
There has been worldwide condemnation of the violence.
UN Secretary General Ban Ki-moon urged the Guinean authorities to exercise maximum restraint, while the West African regional body Ecowas is reported to be pursuing sanctions against the military regime.
The African Union has now expressed grave concern over the latest violence, condemning the "indiscriminate firing on unarmed civilians".
According to Africa analyst Paul Melly, the AU declared sanctions against the leading figures of the regime earlier this month in an attempt to dissuade Capt Camara running for president.
He said following the military's capture of power after the death of long-time ruler Lansana Conte, it was hoped Guinea's human rights record would improve.
"We were already getting signs that this wouldn't in fact happen, but now we've seen a repetition of the army's traditional resort to violence when facing protest," he told the BBC's Network Africa programme.
The military takeover initially had some popular support, but in recent weeks there have been several anti-government protests.
Guinean officials and former aides of Capt Camara have been accused of corruption and links to the drugs trade, including the son of former President Lansana Conte, who was shown confessing on TV to smuggling cocaine.
Guinea expert Gilles Yabi told the BBC's Focus on Africa programme that the rally was "only the beginning" of demonstrations and counter-demonstrations that can be expected in the next few months.
Should Capt Camara stand for president, he said, it would be a violation of the tacit agreement between military and civil forces which has kept him in power.
And it would mark a perpetuation of the kind of rule that Guinea has seen for the past decade - which the military had promised to sweep away.
Source BBC Africa
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