The Abbott government is relishing the prospect of a fresh Senate election in Western Australia, claiming it will be a referendum on its carbon tax repeal legislation.

The Australian Electoral Commission (AEC) on Monday declared the final result with Liberal senators David Johnston, Michaelia Cash and Linda Reynolds and Labor senator Joe Bullock keeping the seats they won at the original count.

The Greens' Scott Ludlam and the Australian Sports Party's Wayne Dropulich claimed the seats which had been initially awarded to Labor's Louise Pratt and the Palmer United Party's (PUP) Zhenya Wang.

The official declaration starts a 40-day clock toward a possible challenge to the result in the Court of Disputed Returns, after 1255 formal ballots and 120 informal votes had disappeared between the original count and recount.

Former federal police chief Mick Keelty will on Tuesday start a two-week investigation into the missing ballots and his finding will underpin whether the AEC will challenge the outcome of the vote in court.

The AEC and other potential parties to the case, the ALP and the PUP, are also considering whether to petition the court.

The court could let the result stand or order a fresh election of all six Senate positions in WA.

Electoral commissioner Ed Killestyn appeared to concede this on Monday, saying there was a "nagging and almost irreconcilable doubt" about the outcome.

He apologised unreservedly to WA voters who had been "disenfranchised" by the loss of the ballots.

Finance Minister Mathias Cormann, a WA senator, said a fresh Senate election in his state - which has a massive mining and energy industry - would be another referendum on Labor's carbon tax.

"It will be another opportunity for the people of Western Australia to send a strong and clear message to Bill Shorten that they want the carbon tax gone," he said in Canberra.

The Labor opposition has said it won't repeal the bills unless the government agrees to proceed to an emissions trading scheme - an option the coalition has rejected outright.

"We will argue that case in any by-election, any general election that comes our way," opposition climate spokesman Mark Butler said.

A fresh election could allow the government to pick up an extra spot in the upper house, making it a little easier to push its repeal bills through after the Senate changeover on July 1.

But Labor could find itself embroiled in an internal battle over its candidate list.

Senator Pratt, who was controversially bumped to Labor's number two spot on the senate ticket behind Senator-elect Bullock, said she would stand if a new WA poll was called.

"There would have to be some flexibility about what political parties put forward for any prospective ballot. In some situations they would have to (change)," Senator Pratt said.

Senator Ludlam believes court action is almost inevitable and appropriate.

WA's chief electoral officer Peter Kramer said the commission was "horribly disappointed", but would be able to run any fresh election very quickly.

PUP leader Clive Palmer says the AEC is conspiring to deny his party the balance of power in the Senate after the recount cost Mr Wang his seat.

"It indicates our voting system isn't fair and it indicates the powers at be don't want to see someone else have the balance of power in Australia, that's what it boils down to," Mr Palmer told AAP.

Mr Palmer said his party was planning to lodge an appeal in the Court of Disputed Returns.