The claims emerged from a Taliban commander during an interview conducted by an Afghani journalist recorded on behalf of the ABC.
Mullah Mohammad accused the SAS soldiers and Australian commandos of killing innocent civilians during clashes.
He claimed the troops caused much damage and killed many villagers.
The accusation comes after it was revealed Australian commandos battled hundreds of Taliban fighters and flew helicopters under enemy fire to evacuate wounded coalition soldiers in recent tough fighting in Afghanistan.
"The ADF rejects the allegations made by the Taliban in the ABC report today," a Defence spokesman said in a statement.
He said the Taliban is the enemy of the Afghani people and is opposed to the democratically elected government in Kabul.
Prime Minister John Howard has defended Australia’s special forces troops in Afghanistan.
"I am certainly not aware of that and nobody's suggested to me that that has happened, and I would be very confident in saying that Australian special forces behave with the utmost courage, the utmost decency and in the best tradition of Australia's military forces," Mr Howard told reporters in Melbourne.
The ADF said it will investigate any allegation that is made through the established process.
But said as yet “no representations” had been made to coalition authorities.