Two bombs dropped on the Great Barrier reef during a botched military exercise have been recovered and disposed of, while two others will remain on the sea floor.

US warplanes were forced to drop four bombs after they ran dangerously low on fuel during a problem-plagued training exercise in central Queensland in July.

Two of the bombs did not contain explosives and the other two were without their fusing mechanisms.

The two live bombs were located by divers on Thursday and Friday and sent to the surface using lift balloons before being destroyed.

After liaising with authorities, the US navy decided to leave the inert explosives, which were filled with cement, on the reef, saying they posed no threat.

Great Barrier Reef Marine Park Authority chairman Russell Reichelt says he was happy with the response.

"Survey images confirm the ordnance landed on a sandy bottom, well away from coral and any sensitive habitat," he said in a statement.

"Our personnel will continue to monitor the area in the coming days for any potential impacts following the recovery and disposal part of the operation."

The US planes were unable to drop the ordnance where they had intended to during the July training exercise 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.

The bombs were dropped during a training activity prior to Exercise Talisman Sabre, a joint war games involving US and Australian troops.