The television report said US soldiers burnt the bodies for hygienic reasons but then a US psychological operations unit broadcast a propaganda message on loudspeakers to Taliban fighters, taunting them to retrieve their dead and fight.
In Washington, the US Defence Department expressed concern over the report and promised that it would be "aggressively investigated".
"These are very serious allegations and, if true, very troublesome," Pentagon spokesman Bryan Whitman told reporters.
"It is the policy of the United States, as well as the Defence Department, to treat all remains consistent with the Geneva Convention and with the utmost respect. These allegations will be aggressively investigated and, if proven to be true, the individuals will be held appropriately accountable," Whitman said.
The "Dateline" current affairs programme on the ethnic Special Broadcasting Service said the story was filmed in early October. The footage of the burning corpses was shot by Australian photojournalist Stephen DuPont who was embedded with a US unit.
"It is the policy of the United States to treat all remains consistent with the Geneva Convention and with the utmost respect"
Dateline said the two Taliban fighters burnt on hills above the village of Gondaz north of Kandahar were killed by the US soldiers the night before.
The footage showed flames licking two charred corpses, their legs and arms outstretched, and a group of five US soldiers standing watching from a rocky ledge.
Footage showed two US soldiers reading two messages from a notebook that they said had earlier been broadcast.
"Attention Taliban you are cowardly dogs," read the first soldier, identified as psyops specialist Sargeant Jim Baker.
US-led forces invaded Afghanistan
in response to the 9/11 attacks
"You allowed your fighters to be laid down facing west and burnt. You are too scared to retrieve their bodies. This just proves you are the lady boys we always believed you to be."
The other unidentified soldier read a second message, part of which said: "You attack and run away like women. You call yourself Talibs but you are a disgrace to the Muslim religion, and you bring shame upon your family. Come and fight like men instead of the cowardly dogs you are."