If the casualties are confirmed, it would be the largest loss of civilian life in a single attack since US troops invaded Afghanistan in 2001.
Al Jazeera's Nick Clark, reporting from Kabul on Thursday, said there were a number of conflicting accounts of what had occurred.
"The provincial governor told us that no one consulted him about the air strikes," he said.
"It's also been reported that the Taliban themselves killed villagers ... There is one account of how they herded together three families and put them in a room and chucked a grenade in there."
Our correspondent said there were also accusations that Taliban fighters had been using the local villagers as human shields.
"Hopefully, this [US-Afghan investigators'] delegation that is in Farah will give us some kind of clue, some kind of answer to what has transpired," he said.
"They'll almost be taking a census of the survivors in the village, they'll be taking eyewitness testimonies ... and also they'll be undertaking the grisly task of examining bomb craters to establish if there are any human remains."
During a visit to Kabul on Thursday, Robert Gates, the US secretary of defence, expressed regrets for all civilian deaths caused by multinational forces in Afghanistan.
However, he said he had heard reports that the Taliban threw grenades into houses in Bala Baluk during Monday's clashes to create casualties that could be blamed on American forces.
|Villagers hold what they say are parts of the missiles that were fired [EPA]
"We all know that the Taliban use civilian casualties and sometimes create them, to create problems for the United States and our coalition partners. We will have to wait and see what happened in this particular case," Gates said.
The US and Nato forces commander in Afghanistan earlier said it was unclear whether the deaths resulted from US military action.
General David McKiernan said US forces launched air raids as they came to the aid of Afghan police who may have been ambushed by the Taliban.
He said the Taliban beheaded three civilians, possibly to lure in the police.
"We have some other information that leads us to distinctly different conclusions about the cause of the civilian casualties," McKiernan said.
Abdul Rauf Ahmadi, the police spokesman for western Afghanistan, has told the AFP news agency that up to 30 of the dead were suspected Taliban fighters and the remainder were civilians, including children, women and elderly people.
Amin, the Farah governor, has said Taliban fighters were reportedly using civilian homes to shelter from US-led forces during the operation targeting fighters.
The US government has come under increasing criticism during the past year for civilian deaths during operations against Taliban and al-Qaeda fighters in Afghanistan.
Barack Obama, the US president, on Wednesday expressed regret for civilian deaths in Afghanistan, vowing to "make every effort" to avoid them in the future.
Washington has heightened its focus on fighting the Taliban since the Obama administration assumed power this year, with an added 21,000 troops due to be sent to Afghanistan.