Around 150 medical practitioners from the group Doctors For The Family have signed a submission to the Senate inquiry into marriage equality opposing same-sex marriage.
The group says it believes heterosexual marriage is healthier for children.
Doctors for the Family's convener Lachlan Dunjey has told ABC News Radio the group is concerned about the health consequences for children of gay marriages.
"It's well proven that children who grow up with a mother and a father in a biological mother and father family do better than children who don't have the opportunity to grow up in that kind of family," he said.
But Australian Medical Association president Steve Hambleton has rejected the claims, saying there is no evidence suggesting children with same-sex parents are any different to those with heterosexual parents.
"There is a growing body of evidence that says there's no difference in their psychological development, their general health, their sexual orientation," he said.
He says the opinions expressed in the submission do not reflect the views of the wider medical community.
Greens Senator Sarah Hanson-Young has dismissed the submission and says discrimination within the Marriage Act should end.
"A child being brought up in a loving home is far more important and that quality of parenting is far more important than any of the criticisms that have been waged by this group of individuals," she said.
The Deputy Chief Minister of the Australian Capital Territory, Andrew Barr, is openly gay and says the doctors' arguments are ridiculous.
"I think that's one of the more ridiculous propositions that's ever been put in Australian public debate. I don't know who these doctors are but it certainly doesn't accord with every other piece of research that's out there on this issue," he said.
A member of Victoria's Human Rights and Equal Opportunity Commission is among the doctors who signed the petition.
Professor Kuravilla George is Victoria's deputy chief psychiatrist and was appointed by the State Government to the board of the Human Rights and Equal Opportunity Commission.
A spokesman for Victoria's Mental Health Minister Mary Wooldridge says the government was unaware of the submission and is seeking an immediate explanation.
Professor George has declined the ABC's request for an interview.