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.

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.

Mr Storer was forced out of the party after he made an earlier shock bid to seize Mr Xenophon's seat, which instead went to former staffer Rex Patrick.

Mr Storer argues he is entitled to take Ms Kakoschke-Moore's spot and sit as an independent. But lawyers for Ms Kakoschke-Moore argue she should be able to reclaim the seat because Mr Storer has left the party and she has now renounced her foreign ties.

But the government has told the High Court it agrees with Mr Storer.

"Ms Kakoschke-Moore's submission that the return of Mr Storer would not give effect to the true legal intention of the voters should be rejected," the submission on behalf of the Attorney-General states.

"Acceptance of that submission would be productive of uncertainty and instability, and would expose the result of elections to manipulation."

While Ms Kakoschke-Moore argues that giving Mr Storer the job would be a distortion of the will of the people, the government disagrees.

"If a sitting senator resigns from their party and becomes an independent, they do not thereby vacate their place in the Senate," the submission states. "The position is no different if, after the voters have expressed their intention by voting, a candidate ceases to be a member of the political party that endorsed them prior to the election."

The full bench of the High Court will hear the matter next month.