Mr Karzai visited the families of the victims in Farah province on Tuesday
The US military says at least 20-30 civilians may have died in a disputed US attack on Taleban fighters in the west of the country earlier this month.
The findings contradict the Afghan government's claim that up to 140 civilians died in the US attacks on two villages in Farah province on 4-5 May.
The US said the preliminary findings also show that 60-65 Taleban insurgents were killed in the attacks.
The deaths led President Hamid Karzai to call for a halt to US air strikes.
"The investigation team estimates that 60-65 Taleban extremists were killed in these engagements, while at least 20-30 civilians may have been killed during the fighting," the US military statement said.
"A review of the physical evidence is inconclusive in determining the exact number of civilian and insurgent casualties," it added.
During a visit to the families of the victims on Tuesday, President Karzai urged American forces to distinguish between villagers and militants.
"All those people who wear a turban and local clothes are not Taleban," he told the gathering.
Mr Karzai, who faces a presidential election in August, has been trying to quell mounting public anger over the loss of civilian lives.
Afghans blame US air strikes for the deaths and destruction in two villages in Bala Buluk, which - if confirmed - would make it one of the deadliest such incidents since the US-led invasion in 2001.
But the US military says a review of audio and video recordings from its aircraft shows that troops were targeting suspected Taleban militants who were fighting from inside village homes or sheltering there as they fled from the aerial strikes.
US officials said their investigators would continue trying to confirm the casualty figures.