The ACT parliament passed a bill in October making the territory the first part of Australia to legalise same-sex weddings.
But the national government challenged the decision, saying it was inconsistent with federal laws.
Some 27 couples who married since the law came into effect last weekend will now have their unions declared invalid.
The legislation had allowed gay couples to marry inside the ACT, which includes the Australian capital, Canberra – regardless of which state they live in.
Federal law, however, specified in 2004 that marriage was between a man and a woman.
Civil unions are allowed in some states in Australia.
Participants in a pro-marriage equality rally march through the streets of Sydney on 12 May 2012
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