Concerns that gay partners under 18 could be "married" under an ACT move to legalise same-sex unions is one reason the plan was rejected by the federal government.
Federal Attorney-General Philip Ruddock has announced that the Commonwealth will override the ACT government bill for a second time.
The federal government vetoed the territory government's efforts to legalise same-sex unions last June, worried it would undermine the institution of marriage.
The ACT government then made several changes to the wording of the bill, including replacing the term "civil union" with "civil partnership" so that it was not confused with marriage.