In the Bedraou valley on 6 April, the boys, who were aged between ten and 15, were found riddled with pieces of shrapnel. Of the group of five adolescents, one survived and his testimony from his hospital bed was a key part of the enquiry.
"This is the first time, to our knowledge, that such a thing has happened involving French forces," said French army spokesman Christophe Prazuck.
He said the teenagers were about 15 metres from some insurgents who were being targeted, but they were hidden by trees.
Meanwhile, on Thursday protesters in the eastern city of Jalalabad chanted slogans and gathered around the body of a man who was killed after a US raid.
US troops raided the home of a Safia Sidiqi, an Afghan MP, and killed one of her relatives. Sidiqi says Nato troops entered the house in the middle of the night.
"My brothers thought it was burglars," Sidiqi said. "One of my neighbours picked up a weapon and went outside the house. The soldiers killed him."
A spokesman for foreign forces in Afghanistan said Western and Afghan troops had raided a house in the area and shot dead an armed man but did not comment on whether the house belonged to a member of parliament.
According to a United Nations study in January, 2,412 civilians were killed in Afghanistan in 2009, a 14 per cent increase on the previous year and the highest toll since the war began in 2001.
Afghan President Hamid Karzai accused Nato forces of having killed four civilians opening fire on a bus earlier this month.
Earlier this month the US military admitted that two pregnant women and a teenage girl were killed by US Special Forces in a raid on an Afghan home in Khataba in February.
At first the military said the women were discovered bound and slain by the Americans, but after an enquiry it emerged US troops had shot them then carved the bullets out of the bodies with knives to remove the evidence.
An Afghan police commander and a government prosecutor also died in the raid.