After several attempts, the jets were running low on fuel and could not land with the bombs they were carrying.
"Due to low fuel and inability to land with the amount of ordnance they were carrying, the on scene commander determined it was necessary to designate an emergency jettison area for the ordnance," Commander Marks said.
He said each bomb was jettisoned in a "safe, unarmed state and did not explode".
"The US Navy and Marine Corps are working closely with Australian authorities to investigate the incident."
The Australian Defence Force said the bombs posed "minimal risk or threat to the public, the marine environment or civilian shipping transiting the reef area".
"The incident is being investigated by the US and findings will be provided to the Great Barrier Reef Marine Park Authority so that the way ahead can be mutually agreed," a spokesman said.
"Defence is working closely with the US military, the Australian Government and environmental organisations to ensure there is no danger to the public or the environment now or in the future."
The Great Barrier Reef is the world's largest coral reef. It is home to more than 3000 individual reef systems and hundreds of tropical islands.
The US Navy is considering how to recover the bombs, which were dropped in a "deep channel" about 16 nautical miles south of Bell Cay, off the Capricorn Coast between Mackay and Rockhampton.
"The safety of personnel and the environment are our top priorities," Commander Marks said.