Addressing the Queen at the Diamond Jubilee Parade and Muster military tribute in Windsor, General David Richards said: "Prince Harry's success in flying training means it is likely he will serve operationally again."
It is the first time such a senior military figure has given such a clear indication of 27-year-old Harry's future deployment, the Daily Mail reported.
Harry's return to the war zone will again raise fears he would be a 'trophy' target for the Taliban.
Harry, third in the line of succession, has been on "limited combat ready" status since February, which means he could be sent to Afghanistan with 662 Squadron.
He was last in Afghanistan in 2008, but flew home when news of his deployment broke in the media.
Prince Harry qualified as an Apache helicopter pilot in February this year after 18 months of training in the UK and US.
Prince Harry was a high-flyer during his Apache training, qualifying top of his class, which is a huge achievement given how notoriously difficult these airborne tanks are to master.
Captain Wales, as he is known in the Army air corps, was presented with the best co-pilot gunner award during a dinner to mark the end of his course.