D'Arcy and Monk posed with the weapons in a gun shop in the US where the Australian swimming team had been training and competing before the Olympics start next month.
D'Arcy, who described the shooting experience as "pretty fantastic, apologised for causing any offence.
"We got the opportunity to fire a couple of guns which was pretty fantastic to be honest because we don't get that opportunity back home," D'Arcy told reporters at Brisbane Airport after the pair returned to Australia on Friday.
"It was all just meant to be a bit of fun, the photos were just a bit of fun.
"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.
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