"If anyone's been offended I deeply apologise. It was never the intent, it was never supposed to be offensive."
Monk, who took them off his Facebook page, also apologised.
"I deeply am sorry and I'm sorry if I offended anyone out there," he told reporters.
In the photo taken by the gun shop owner, D'Arcy is smirking as he holds up a pair of automatic pistols, while Monk smiles broadly holding two pump-action shotguns across his chest.
Swimming Australia (SA) ordered the pair to remove the photos from their Facebook and Twitter accounts under their social media policy.
The Australian Olympic Committee (AOC) has said it will await SA's investigation before considering sanctions.
Australia's chief de mission for the London Games, Nick Green, described their actions as foolish and a pre-Games lesson on the perils of athletes using social media.
D'Arcy is a medal hope in the 200m butterfly in London, while Monk will compete in the 200m freestyle and Australia's well credentialled 4x200m freestyle relay team.
Neither is new to controversy.
D'Arcy was kicked off the 2008 Australian Olympic team after assaulting former swimmer Simon Cowley in a bar, leaving him with multiple facial injuries.
Last year, Monk told police he was the victim of a hit and run accident but later confessed he suffered his injuries when he fell off his skateboard.
- AAP
