Brigadier General Carter Ham, deputy director of the Joint Staff, said US troops were on the ground at the village of Azizi, southwest of Kandahar, to assess the situation.
"When such allegations surface we take those very, very seriously and investigate those to the fullest," he said at a Pentagon press conference.
He said the US military takes care to avoid civilian casualties.
"Having said that, it's also important to note the Taliban knows that. And it's not unusual at all to see them operating in and amongst non-combatants knowing the great measures we take to try and protect non-combatants," he said.
President Hamid Karzai ordered an investigation following reports from Afghan officials and residents of heavy civilian casualties from the air strikes, which Ham said were carried out mainly by A-10 ground-attack jets.
Kandahar province's governor has said at least 16 civilians were killed in the operation but villagers and a rights official have said the number is higher.
Governor Asadullah Khalid said Taliban rebels had hidden in villagers' homes, accounting for some of the civilian deaths.
A teacher in Tulakhan village in Panjwayi district told AFP by telephone that he saw the bodies of 40 civilians, including children, and about 50 others had been wounded in the coalition strike.
The air strikes came amid intensifying fighting in southern Afghanistan, where Taliban fighters have launched a spring offensive.
Ham said the Taliban were responding to Afghan security force moves into areas they have never entered before and to a transition from US to NATO forces in the south.
"I think again the Taliban see that and say, if they don't do something to disrupt that transition to NATO control they may lose the opportunity to do that for a while," he said.