The US 7th Fleet had earlier said only that the planned target range was "not clear of hazards" at the time, forcing the two Harrier jets to dump their ordnance within the Great Barrier Reef Marine Park off Queensland state.
But Commander William Marks revealed Monday that the crews had made the decision, which has been criticised by environmentalists, because civilian vessels were detected inside the drop range.
"The approved area where they could do some of this live training with these 500-pound bombs, it was not safe to drop the bombs," he told the Australian Broadcasting Corporation.
"There were civilian boats right below them."
The joint Australia-US training which began on July 15 involves 28,000 troops and Marks was unable to say how civilian vessels had strayed into the Shoalwater Bay military training area.
"I don't have any more information about what they were doing and why they were there," Marks said.
"But it's part of our procedures just to do that safety check and if we do see that, then for safety reasons we do not drop any ordnance."
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 on 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. Running low on fuel, and unable to land carrying such a large load, they decided to jettison the bombs.
"Their priority was to get to a place which would create the least impact, which we believe we did -- dropping them in between 50 and 60 metres of water in a place where it is not a hazard to shipping and not a hazard to navigation," Marks said.
The drop was coordinated with Australian authorities, he said, adding that the environment was a priority for the US military.
The Great Barrier Reef Marine Park Authority, which will work with the defence department to recover the bombs, said they were considered low risk and about 30 kilometres from the nearest reef.
But the Queensland Greens Sunday described the incident as outrageous.
"Is this how we look after our World Heritage area now? Letting a foreign power drop bombs on it?" asked Senator Larissa Waters.