Federal Parliament has passed legislation to remove the power of federal ministers to veto territory laws.

The legislation means territory laws can now only be overturned by a vote of both houses of federal Parliament and not by individual ministers.

It is the first Greens bill to pass the Parliament, and party leader Bob Brown says it is a significant day.

"[This is a] very important milestone for democracy in the territories," he said.

The Opposition tried to amend the legislation to make sure the laws could not be used to legalise same-sex marriage.

But Labor frontbencher Craig Emerson has told Parliament that federal marriage laws would still stand.

The Government says it has clear legal advice that the Opposition amendments are unnecessary.