But gay rights groups claim the laws don't contravene federal laws on marriage.
The ACT Parliament has voted to allow gay couples to enter into a civil union, but the Prime Minister, John Howard says such unions are unacceptable.
The Federal Attorney General Phillip Ruddock will direct the governor-general to scrap the ACT laws.
Mr Rodney Croome from the Gay and Lesbian Rights Group says the Prime Minister's assertion that civil unions in the ACT contravene the National Marriage Act, are untrue.
“It's saying that the ACT law potentially contravenes or contradicts the National Marriage Act and therefore may be constitutionally saying it looks too much like marriage and therefore goes against the spirit of the federal legislation. If there really was a legal and a constitutional issue about the ACT law, then all the federal government needed to do was ask the High Court to strike down the ACT law because it was inconsistent with the National Marriage Act. It hasn't done that because it knows it hasn't got a case,” Mr Croome said.