The US soldier accused of the Kandahar massacre is on his way to the US from Kuwait, where he was being held, and is expected to face a military tribunal there.
Afghan MP’s had demanded the soldier be tried in public in Afghanistan.
Hamid Karzai earlier met relatives of the dead, who demanded justice.
Men, women and children were shot and killed at close range as the US soldier apparently went on a rampage in villages close to a NATO base in the remote Panjwai district of southern Kandahar province.
He also said the problem of civilian casualties at the hands of NATO forces had “gone on for too long”
“This is by all means the end of the rope here,” Hamid Karzai said.
On Wednesday Hamid Karzai told the US that it must pull back its troops from village areas and allow Afghan security forces to take the lead, in an effort to reduce such civilian deaths.
The Taliban also called off peace talks in the wake of the killings although they made no mention of the massacre in their statement.
Earlier, the president met relatives of those who had been killed last Sunday. The assembled villagers berated him and urged him to seek justice.
Some of the villagers believe there was more than one gunman, an allegation that has repeatedly contradicted the official version since Sunday when the shootings took place. He assured villagers that he would pursue that allegation.
Hamid Karzai listened as surviving family members from the Kandahar massacre gave their versions of the murders during a meeting in a grand hall in the presidential palace.
“Why did this happen?” demanded one man who lost nine members of his family. “Do you have answers, Mr. President?”
“No, I do not,” responded a tired-looking Hamid Karzai.
Some details about the alleged killer also emerged from John Henry Browne, the lawyer who said he represented him.
John Henry Browne said the soldier – who has not been named – had received body and brain injuries while serving in Iraq and had been unhappy about doing another tour of duty.
Speaking in Seattle, where the accused soldier is based at Joint Base Lewis-McChord, John Henry Browne denied reports that the accused had problems either with alcohol or his marriage.
Earlier on Friday, a NATO helicopter carrying Turkish troops crashed into a house on the outskirts of the capital Kabul, killing at least 12 soldiers and two children on the ground.
The death toll is the heaviest single loss of life so far for Turkish troops in Afghanistan, of whom there are currently more than 1,800.
Despite the recent string of setbacks, such as the suspension of peace talks by the Taliban, the US has stressed that it remains committed to Afghan reconciliation.
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