Doctors said the Department of Health briefed them last month about a clause it had added during legislative changes made to recognise the parents of children born through surrogacy.
It said the law gave it the power to request identifying information about anonymous donors if it was applied for by related individuals, such as the child conceived using the donation.
The Health Department said it would not, and could not, legally hand over the private information about the donors to any offspring, but fertility experts have questioned why it needs to collect it at all.
Peter Illingworth, the president of the Fertility Society of Australia and a specialist with IVF Australia, said the department has introduced the clause without consultation.
''When the initial act was set up it was done with widespread consultation,'' he said. ''We are left wondering what the government's motivations were in making this change.''
A spokesman for the department said the clause was inserted because the government believed it would need as much information as possible to match donors and offspring on a voluntary database it runs.
''We can't release the information at all without the donor's consent and it is as simple as that,'' he said. ''Consent over-rides everything.''
He acknowledged information such as the names or addresses of donors would not be very useful for that, and so the department had committed to only request de-identified information such as donor number and blood type.
For the past 10 years fertility clinics have allowed donations only from men who are happy to have their identity disclosed, Associate Professor Illingworth said. But as a result sperm donations had more than halved between 1998 and 2008.
IVF Australia was advertising for men on smh.com.au, and a similar campaign last year produced 50 inquiries and 14 suitable donors.
Mark Bowman, the medical director at Sydney IVF, said people who donated in the past were generally younger with less life experience and understanding of what they were doing. Often university students were targeted for donation.
''They were making a decision at 21 or 22 and they hadn't had their own children,'' he said.
''They were told it was anonymous, you were helping people and you were leaned on heavily to do it.''
He also questioned the department's motivation for the change.
Caroline Lorbach, a spokeswoman for the Donor Conception Support Group, said almost all children conceived using donors believed they should have the right to know the identity of their biological parents.
''They are asking for information that is already held by doctors and they feel terrible someone has the right to information withheld from them,'' she said.