The Court of Disputed Returns has given a strong indication that Western Australia will go back to the polls for a new Senate election.

The Australian Electoral Commission (AEC) asked for the Senate election to be declared void after 1,370 ballot papers were missing for a recount.

Justice Kenneth Hayne has ruled that the loss of those ballot papers meant the electors were prevented from voting.

He also ruled that Greens senator Scott Ludlam and the Australian Sports Party's Wayne Dropulich were not duly elected.

Submissions from the Labor Party and the Palmer United Party (PUP) that the first result be upheld were dismissed.

That first count resulted in success for three Liberal candidates, two from Labor and one from the PUP.

The result was challenged by Senator Ludlam and Mr Dropulich, and a recount was ordered in which they were successful.

But Justice Hayne found the two were not duly elected:

It is not possible to determine who was duly elected because ballot papers have been lost.

It is not possible to determine who was duly elected because ballot papers have been lost. All parties rightly accepted that, if the court declares that Mr Dropulich and Senator Ludlam were not duly elected, and cannot declare who was duly elected, the only relief appropriate is for the election to be declared void.

Justice Hayne did not, however, declare the election void at this stage.

Senator Ludlam told the ABC's 720 Mornings program the judge ruled out a number of options.

"He certainly hasn't confirmed that there will be a new election," he said.

"What he's done is he's ruled very clearly on the three points of law that he believes the case hinges on and he's agreed substantially with the Electoral Commission and the Australian Greens.

"It's now left to the petitioners to argue what they think should happen next.

"It's our view that it looks very likely that we're going back to the polls on the basis of the fact that he ruled out a number of other options on the way through this morning."

Missing ballot papers the key ruling

Sorry, this video has expired Antony Green says new election can not be planned until existing result is voided

ABC election analyst Antony Green says the key ruling today was the court stating that the missing ballot papers were a denial of the vote to those people.

He says that makes it much more likely the court will now go down the path of voiding the election.

He also referred to the constitution, which states that senators are elected from the state as one electorate, and because the proportional representation system means the election of those six members is inter-related, voiding the election voids all six seats.

Mr Green says he thinks the process has come in two steps to give the parties a chance to respond.

Clive Palmer, the MP for Fairfax and PUP leader, says heads should roll at the AEC.

"The AEC Commissioner and the others responsible for this debacle should resign as no-one can have confidence in the AEC following the events of the past few months," he said.

"Someone should be accountable for this mess."

PUP candidate Dio Wang won the fifth Senate seat in the initial count, but lost it in the recount.

WA Premier Colin Barnett says if the High Court does order a new election, voters will be less inclined to turn out to vote.

"The difficulty will be to get people interested in a re-run of the Senate election," he said.

"That will be a problem for the Electoral Commission, to get people to actually go out and vote."

Mr Barnett says there may also be a swing to major parties.

"I believe what you may well see here is a lower vote for small parties and independents and a return of the vote to the two major parties, Liberal and Labor," he said.

Justice Hayne has adjourned the matter until Thursday.

Read the High Court statement here.