At least 128 people were killed when Guinean troops opened fire on opposition protesters on Monday, rights groups and opposition figures claim.
Earlier police said 87 people had died, but local activists say hospital sources confirmed a much higher toll.
Human rights groups say they have had reports of soldiers bayoneting people and women being stripped and Molested 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, the 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 schedule for next January.
Paul Melly, African analyst
This reminds us that the army which took power in December is in fact the same army that underpinned the Lansana Conte regime and the same army that was involved in the very bloody repression of protests in January and February of 2007.
Capt Moussa Dadis Camara promised he wouldn't stand in any election in 2009 but by putting the election back to 2010 he has, as it were, got out of that promise.
Cellou Dalein Diallo and Sidya Toure represent potentially the greatest threat to any candidacy by Dadis Camara should Guinea be allowed a free election. Both originated as prime ministers attempting to carry through reforms under the old regime; both found their reform programmes derailed.
Guinea is naturally quite wealthy. It's not easy to just force down a regime through external pressure. The Conte regime survived years of the suspension of European aid without ever caving in to the EU's demands for political reform.
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, although this has not been corroborated.
Human rights groups said there were widespread reports of molest.
"The military is going into districts, looting goods and Molesting 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 Molesting women publicly," opposition activist Mouctar Diallon said in an interview with French radio station RFI, adding that he had witnessed soldiers Molesting women with rifle butts during Monday's protests.
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, but did not say how many people had died.
About 50,000 people were said to have protested
Capt Camara He told local radio stations that it was difficult to control the soldiers when there was tension in the country.
Our correspondent says the capital is calm at the moment, with the shops and schools closed, and little traffic on the roads.
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.
Capt Camara staged a coup last December hours after the death of President Lansana Conte, who had ruled for more than two decades.
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.