"I take this possible loss of life or injury to innocent Afghans very seriously."
The attack was carried out by a US F-15E Strike Eagle jet that dropped 225kg bombs on two fuel tankers that had been hijacked by the Taliban but had become stuck in mud while being driven over a river.
It was unclear how many of the dead were fighters and how many were villagers who had been siphoning fuel from the lorries at the offer of free diesel from the Taliban.
One boy told an Isaf delegation visiting the wounded: "I went to get the fuel with everybody else, and then the bombs fell on us."
Villagers went ahead and buried their dead in at least 50 graves.
McChrystal promised to make the findings of the investigation public.
The European Union has publicly criticised the attack, saying it undermines efforts at nation-building in Afghanistan being carried out by EU nations.
Bernard Kouchner, the French foreign minister, said: "This was a big mistake."
"We have to look into this and to denounce those responsible."
As the investigation began, a bomb blast hit a German military convoy, wounding at least three soldiers. The Taliban said it carried out the attack in revenge for Friday's assault.
Abdullah Razaq Yaqoobi, the police chief in Kunduz, said a suicide car bomb caused the injuries, though German military officials blamed a roadside bomb.
The UN mission in Afghanistan, lead by Peter Galbraith, has dispatched its own investigation team, emphasising that "the families of the victims must receive all the help they need''.
Brigadier-General Eric Tremblay, a spokesman for the Nato-led Isaf, told Al Jazeera that they would do whatever was necessary "to investigate and provide as much support as is needed".
|Afghan villagers pray over the graves of the relatives killed in the attack [Reuters]
Robert Gates, the US defence secretary, told Al Jazeera in a first interview since Barack Obama was elected as the US president, that poor relations would make troop increases unlikely.
"I've had a number of reservations about significant additional US troops ... if our forces should come to be seen at some point as occupiers rather than partners", he said.
Afghan anger over civilian deaths caused by international forces compounds the problems being faced by the US administration over rising military casualties.
Many Democratic party members in the US are unhappy with Obama's decision to send 21,000 extra troops to Afghanistan.
Others want the US military involvement scaled down.
But Gates told Al Jazeera that he opposed the idea of starting preparations for a troop withdrawal.
He said he would not talk about victory or defeat but rather about achieving goals.