The death toll would make it the deadliest incident for Afghan civilians since the US-led invasion in 2001.
The US military has acknowledged that "a number" of civilians were killed, but said it was impossible to say how many because all the bodies were buried before investigators arrived.
Colonel Greg Julian, a US military spokesman, said that two US investigations were still under way, one ordered by commanders in Afghanistan immediately after the incident and another ordered more recently by US Central Command, responsible for the wars in both Afghanistan and Iraq.
"No other news makes me as sad and sorrowful as incidents of civilian casualties during military operations"
The villages in the Bala Baluk district of the southwestern province were bombed on May 3 after Afghan forces and US marines became involved in a battle with suspected Taliban fighters.
Witnesses said that villagers were hiding in their homes when the US aircraft destroyed them.
The government compiled a list of the victims which said that 93 of the dead were children and only 22 were adult males.
The Afghan government has paid the relatives of victims the equivalent of about $2,000 for those who were killed and $1,000 for the wounded, the defence ministry said.
Karzai demanded the military halt its use of air raids after the incident, but so far the US military has only agreed to review its operations to try to reduce the risk to civilians.
On Saturday, the defence ministry quoted Karzai as saying: "No other news makes me as sad and sorrowful as incidents of civilian casualties during military operations."
Such incidents have brought repeated condemnation from the Afghan government, which says they are turning people against Karzai's administration and foreign forces operating in the country.