The official, who was not identified, said the attack occurred in a village near Mir Ali in the North Waziristan tribal region and also damaged a nearby house.
"Both of the militants on the motorbike were killed on the spot," the official told The New York Times. "The drone fired two missiles that also damaged a nearby house, but no casualty has so far been reported inside it."
The strike was the second drone attack in North Waziristan this month. The first was on July 2 and left 17 people dead.
The Times said drone activity, which is highly unpopular among Pakistan's government and civilian population, has been less frequent in recent weeks due to greater scrutiny of the program by the Obama administration.