An official in Lower Austria state found no grounds for fear of persecution based on the sexual orientation of the 18 year-old, the Falter weekly newspaper reported.
"The way you walk, act or dress does not show even in the slightest that you could be homosexual," the official reportedly wrote in his assessment rejecting the claim.
The official also found "potential for aggression" which "wouldn't be expected from a homosexual", because the man fought with others in the charity accommodation that houses them.
The Afghan reportedly had few friends and liked spending time alone or in small groups, leading the official to question in his report: "Aren't homosexuals rather social?"
The official rejected the statement that the Afghan had kissed straight men, saying he would have been beaten if he had done so, the Falter reported.
The Afghan had said he became aware of his sexuality when he was 12 years old, but the official found that was "rather early" and so not likely, particularly in a society like Afghanistan "where there is no public sexual stimulation through fashion and advertisement".
The Afghan, who came to Austria alone as a minor, is appealing the decision, the Falter said.
Austria's interior ministry said Wednesday that it could not comment on the specific case, but that it was "not reflective of the (wider) reality". Some 120,000 asylum claims have been decided on over the past two years, it added.
"Asylum-seekers must substantiate their reasons for fleeing. There are no concrete rules of proof, but the authorities must show if and why a claim was found to have been substantiated," the ministry said in a statement, adding "individual impressions" were significant in the interview process.
It said the government is currently working with the United Nations refugee agency UNHCR to offer further training on LGBT issues to "ensure quality" in the asylum evaluation process.
Homosexuality is illegal in Afghanistan's conservative, highly gender-segregated society.