The Australian and US navies are now working to retrieve the ordnance.
Two of the bombs did not contain explosives and the other two were without their fusing mechanisms.
Royal Australian Navy minehunter HMAS Gascoyne found the bombs on Friday.
US warplanes were forced to drop the bombs after they ran dangerously low on fuel during a problem-plagued training exercise in central Queensland last month.
The planes were unable to drop the ordnance where they had intended because civilian vessels had wandered into the pre-approved drop zone.
Instead they were let go in about 50 to 60 metres of water inside the boundaries of the Great Barrier Reef marine park.
Joint Operations Chief Lieutenant General Ash Power says the retrieval will depend on weather conditions and environmental considerations.
‘At no stage did the jettisoned ordnance pose a threat to the safety of people or the Great Barrier Reef,’ Lt-Gen Power said in a statement.
The bombs were dropped during a training activity prior to Exercise Talisman Sabre, a joint war games involving US and Australian troops.