Two Harrier jump jets dumped their ordnance over the world-renowned marine park during a Australia-US training exercise which began on July 15 because civilian vessels were detected inside their original drop zone.
The decision to jettison their load over a World Heritage site was slammed by environmentalists, although the bombs are considered low risk and landed about 30 kilometres from the nearest reef.
The navy said its Japan-based Seventh Fleet, which is taking part in the exercises, would take the lead in the retrieval operation in coordination with Australian authorities.
"We are fully committed to redressing any potential adverse environmental impact in a timely manner."
More From This Section
Detailed recovery plans would be announced later, it added.
Officials on Sunday said the fighter jets had conducted an "emergency jettison" of two BDU 45s, which are inert ordnance, and two GBU 12s, which were dropped in an unarmed state over the iconic reef's marine park on July 16.
The two AV-8B Harrier planes had intended to drop the bombs on a range on a nearby island but were unsuccessful despite several attempts.