The High Court has accepted South Australian senator Bob Day's application to challenge the Government's Senate voting changes.

The Coalition managed to pass the legislation with the support of the Greens and Independent senator Nick Xenophon after a marathon sitting session of more than 28 hours.

Under the new laws, voters who issue a limited number of preferences at the polling booth will have their ballot discarded if their preferred candidates are excluded from the race.

The legislation's aim is to stop the complex preference-swapping deals that led to a number of senators being elected with only a fraction of the popular vote.

"I think today was a really important win in the battle for voters' rights and let's be clear what happened last month in the Parliament, that voters' rights were taken away," Senator Day said.

"Voters who choose to be represented by a minor party or, rather, who do not want to be represented or do not vote for a major party under these new laws, will see their vote, by and large, exhaust."

Day warns against double dissolution

Senator Day warned the Government against holding a double dissolution election in July, with the challenge still looming.

"I think the Electoral Commission has indicated that he certainly would prefer to wait until a judgment has been handed down on this matter before they call an election," Senator Day said.

"It would be very disruptive to have the current Senate voting laws ruled invalid in the middle of an election campaign."

Despite being the only member of the crossbench to put his name to the challenge, Senator Day said he had positive feedback from other crossbench senators since launching the action.

"They're all very supportive of it," he said.

"Naturally, they believe that they were lawfully and legitimately elected and under our Senate voting system and they all voted against the changes that were made in Parliament."

While posing for photographs outside the High Court, Senator Day said he felt like Darryl Kerrigan from The Castle, a movie about a man taking his fight all the way to the High Court and winning.

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A group called the 3 Million Voice Committee has joined Senator Day's challenge, with some of the members of the committee coming from the micro parties Senator Day is seeking to protect.

Earlier, Senator Day told the ABC that he would argue on the potential disenfranchisement of voters, following the High Court's response to missing ballot papers from Western Australia in the last federal election.

"Just 1,200 votes went missing and the High Court was sufficiently concerned about that to order a rerun because of the way it would impact the outcome of the election," he said.

"What their attitude might be to 3 million votes exhausting or dying deliberately as a result of these laws is the question that needs to be asked."

But Special Minister of State Mathias Cormann had said the Government was very confident the reforms were consistent with all the requirements of the constitution.

"The whole purpose of the reforms is to empower voters to directly determine where their preferences go and hence who they ultimately end up helping to elect to the Senate," he said in a statement.

"Under our system the voter has control of what he or she wants to do with their vote all the way through and who they help elect to the Senate. In our opinion that is as it should be."

The case will be heard by Full Court of the High Court on the May 2 — the day before the federal budget is due to be handed down.