A nurse was made to feel like he had a sign that read "kiddie fiddler" over his head after he was moved away from a young girl on a Qantas flight, he said.
Daniel McLuskie said he had a similar experience to a firefighter on a Virgin Australia flight when he was made to switch seats with a woman because he was sitting next to a unaccompanied child.
Qantas has defended its policy, saying it is consistent with other airlines around the world and reflects parents' concerns.
Mr McLuskie, 31, is a senior nurse at the local health district in Wagga Wagga and was flying from the city to Sydney in June when he said he was humiliated by the cabin crew.
He was seated in the second last row of the flight next to a girl he estimated to be about 10 years old.
After the safety demonstration, a flight attendant asked a woman on the opposite side of the aisle to swap seats with Mr McLuskie.
After the plane was in the air and the meals had been served, Mr McLuskie said he went to the back of the flight to ask why he had been moved and was told it was the policy of Qantas not to have men sit next to unaccompanied children.
"There were people that looked during the actual move, people looked at me or looked around because there was a bit of a ruckus at the back of the plane," he said.
"And then the man in front of me throughout the flight kept looking at me and obviously my sense of paranoia was heightened, if you want to call it that, because of what had occurred.
"After the plane had taken off, the air hostess thanked the woman that had moved but not me which kind of hurt me or pissed me off a bit more because it appeared I was in the wrong, because it seemed I had this sign I couldn't see above my head that said 'child molester' or 'kiddie fiddler' whereas she did the gracious thing and moved to protect the greater good of the child."
Mr McLuskie said he has working-with-children checks almost yearly and told the flight staff he found his treatment and the policy insulting and discriminatory.
He asked to speak to a manager when the plane landed in Sydney and was told there was no one available on the weekend who could talk to him.
Instead he was given a customer care card to fill out with his feedback.
Mr McLuskie said he did not hear back from Qantas and followed up his complaint with an email more than a week ago but still did not hear back from the airline.
It was not until he tweeted them last Wednesday - two days before the news broke of Virgin's treatment of one its male customers - that he got a response.
"They got back with a semi-sympathetic apology, if that," he said.
"I was just told it was the policy and it was what people who send unaccompanied minors on flights want and it's not their fault, which I disagreed with at the time...
"I think it absolutely sucks, it's totally and utterly discriminatory in my mind, it's a complete and utter generalisation...
"You don't know who the person is and it's highly unlikely [that a child will be harmed on a flight]. If a child is going to be harmed or hurt it's probably going to be by someone closer to them than a stranger on a flight.
"I was absolutely fuming, I couldn't have been angrier at Qantas."
Mr McLuskie said he would like to see the policy either scrapped completely, have parents fly with their children if they were really concerned or have Qantas chaperones who fly with the child and look after them.
"I hate to say this but it is a sign of that reverse discrimination that occasionally exists out there," he said.
Virgin Australia announced a review of its policy on Friday after a backlash to the story of fireman Johnny McGirr, who was asked to move seats away from two children on a Brisbane to Sydney flight in April.
A Qantas spokesman confirmed the policy, but said it was rare that a passenger was asked to swap seats after boarding the plane.
"Qantas' policy is consistent with other airlines around the world and is designed to minimise risk," he said.
"The policy reflects parents' concerns and the need to maximise the child's safety and wellbeing.
"In most instances unaccompanied children are allocated seats prior to boarding and there are no issues.
"On the rare occasion where a male passenger is seated next to an unaccompanied child, airlines need to take care when moving passengers to ensure this is done discreetly and respectfully."
Qantas policy states that unaccompanied minors must not be seated next to an adult male customer or in an exit row and in some circumstances, a window seat.
Where possible Qantas aims to seat children near crew areas or next to an empty seat.
"We try to pre-seat children in the most appropriate areas, however due to late bookings we will sometimes need to move the child to seat them in a more appropriate area," the spokesman.
In 2010 British Airways changed its policy that men travelling alone could not sit next to unaccompanied children after they were taken to court for contravening the Sex Discrimination Act.
British Airways now seats unaccompanied children in their own area after businessman Mirko Fischer sued the company after flight staff asked him to move away from a child after he had switched seats with his pregnant wife.
BA denied its policy was discriminatory but admitted to sex discrimination in Mr Fisher's case and agreed to pay him £2,161 in costs and £750 in damages.
- Sydney Morning Herald