The helicopter carrying Maj Gen Javed Iqbal, the General Officer Commanding for Swat valley, was fired at in Nusrat Dara area at 11.30 am local time, TV news channels reported.
Iqbal, who has played a key role in directing operations against the Taliban, sustained minor injuries to his right leg.
Iqbal was flown to Rawalpindi by the same helicopter and taken to the Combined Military Hospital.
He was in a stable condition, the channels reported.
There was no official word on the reported incident. No group claimed responsibility for the attack.
The Taliban were flushed out of most parts of Swat following a massive operation in 2009.
However, most of the top militant leaders of the region, including Tehrik-e-Taliban Pakistan commander Maulana Fazlullah, continue to be at large.