The Herald Sun of Australia reported the photos, taken in a gun shop in Santa Clara, Calif., showed Nick D'Arcy with two pistols standing next to Kenrick Monk, holding two shotguns across his chest, CNN said.
The swimmers had been training in the United States for the Summer Olympics in London.
By Friday morning, the photo did not appear on either of the swimmers' Facebook pages.
In a statement, Swimming Australia said it does not condone "the posting of inappropriate content on Facebook, Twitter or any social media platform."
"It was all just meant to be a bit of fun. The photos were just a bit of fun," D'Arcy said after returning to Australia. "If anyone's been offended, I deeply apologize. It was never the intent; it was never supposed to be offensive."
Swimming Australia said it would speak with both swimmers about the photo.
The two swimmers, both named to Australia's team in March, face possible Olympic sanctions, CNN said.
The U.S. Network said dozens of fans said in posts on Monk's Facebook page they support the athletes and Swimming Australia had blown the photo out of proportion.
D'Arcy was removed from the Olympic team in 2008 after being charged with assault for hitting a teammate.