Villagers had claimed civilians were killed in the attack in Kapisa
The US military in Afghanistan is investigating reports that up to 25 civilians were killed in an operation north of Kabul this week.
The US had said a Taleban commander and 18 militants died in Kapisa province.
US Central Command chief Gen David Petraeus has been meeting President Hamid Karzai, who has urged Western troops to reduce civilian casualties.
New US President Barack Obama has backed a 30,000-strong troop surge for Afghanistan this year.
His inauguration has been generally welcomed on the streets of Kabul, although a top Taleban spokesman has again reportedly warned Western troops to leave the country.
Separately, violence continued on Wednesday when a suicide car bomb attack on an Afghan military convoy left two soldiers dead in the west of the country.
The US military had said Tuesday's operation in Kapisa, 50km (30 miles) north of Kabul, killed a key Taleban commander, Mullah Patang.
On Wednesday, US spokesman Col Greg Julian said the coalition would investigate villagers' claims that 25 civilians had been killed.
A senior government source told the BBC that Mullah Patang had been killed along with three bodyguards, but added that a number of other locals had also died in the operation.
He said Mullah Patang had been dining with local people in the village of Inzeray in Tagab district when the house he was visiting was struck. According to the official, US special forces had been dropped from helicopters, before calling in air support.
The BBC's Bilal Sarwary in Kabul says Kapisa is a strategically important province, near Bagram air base and close to the Kabul-Jalalabad highway.
Afghan officials say the district is frequently used by militants as a stopover on their way to carry out attacks in the capital.
Deputy police chief for Kapisa, Naimatullah Hakimi had earlier said meetings were held with elders to find out who died and he insisted that "no civilians were killed".
The news of the investigation comes only a day after Mr Karzai addressed the Afghan parliament and once again urged US-led and Nato troops to do more to reduce civilian casualties.
Mr Karzai, who is due to face a presidential election this year, said the fight against militants could not be won without popular support from Afghans.
"We don't accept civilian casualties in our land in the war on terrorism," he told parliament.
Late on Tuesday Mr Karzai met Gen Petraeus, who had arrived from a trip to Pakistan where he announced a new supply route to Afghanistan had been agreed with Russia and Central Asian states. The Pakistan route has suffered militant attacks.
Mr Karzai's office said he had again stressed to Gen Petraeus the need to avoid civilian casualties.
Mr Karzai also called for Afghan forces to be boosted with training and equipment and said the trust of the Afghan people must be won, the office said.
President Barack Obama has said Afghanistan is one of his top priorities.
The 30,000 extra troops will join 33,000 US and 32,000 other Nato troops already in the country.
President Karzai said Mr Obama's inauguration was the start of a "promising new era of understanding" between Kabul and Washington.
The inauguration was also welcomed by many ordinary Afghans on the streets of Kabul.
Hamid Karzai says civilian casualties must be reduced
The BBC's Bilal Sarwary says there was a sense of jubilation among many he spoke to.
Labourer Mohammad Gul said: "I have a lot of hope from Obama. Each time he talks on television, he seems like a honest person. Bush came across as bad guy in the movies.''
Eighteen-year-old Akmal said: "Obama is a very likeable president... I am hoping that he will help our army, police and government."
But the new president was also given a warning by a spokesman for the Taleban.
Qari Yousuf Ahmadi told AFP news agency that Mr Obama should pull out Western troops.
"We have no problem with Obama. However he must learn lessons from [former US president George W Bush] and before that the Soviets," he said.
"The only solution is that they leave Afghanistan."
Mr Ahmadi is a regular spokesman for the Taleban but analysts say the organisation is no longer a single entity in Afghanistan and has many different groups.
In Wednesday's suicide attack, two Afghan soldiers were killed when the bomber detonated his explosives next to an army vehicle in Herat province, the defence ministry said.