Nick Xenophon's influence in the Senate is under increasing threat after the federal government backed a defector's bid to seize one of his party's seats.

While Senator Xenophon resigned last year to rejoin South Australian politics, his party still held three seats on the Senate crossbench – making it a significant voting bloc.

Senator Skye Kakoschke-Moore announces her resignation in November, alongside party leader Nick Xenophon. Credit:AAP

But then junior senator Skye Kakoschke-Moore quit in November after discovering she was a British dual citizen, putting one of those three seats in doubt.

While the seat would normally go to the next person on the Nick Xenophon Team ticket, the case has been complicated by the fact that former candidate Tim Storer is no longer a member of the party. So now it will be up to the High Court to decide how the vacancy is filled.