The result of the West Australian Senate vote recount is set to be revealed this weekend amid concerns that more than 1300 missing ballots may mean the state has to go to a new election.

The Australian Electoral Commission (AEC) directed a recount of some WA Senate ballot papers, prompted by the close result of just 14 votes for the sixth Senate seat and appeals by the Australian Greens and Australian Sports Party.

During the recount, that looked at informal votes and 1.2 million above-the-line ballot papers, 1375 votes which had been verified in the initial count could not be "located, rechecked or verified in the recount process".

The AEC apologised and has hired former Australian Federal Police commissioner Mick Keelty to independently, and urgently, inquire into the matter.

Meanwhile, the AEC WA manager Peter Kramer says the results of the recount and distribution of preferences will be known on Saturday afternoon and the candidates have been asked if they want to appoint scrutineers to observe the distribution of preferences.

But some politicians including Australian Greens Senator Scott Ludlam, and Palmer United Party leader Clive Palmer have decried the process.

Mr Palmer believes the original election result should stand.

The initial result gave seats to the Palmer United Party's Zhenya Wang, Labor's Louise Pratt and Joe Bullock and the Liberals' David Johnston, Michaelia Cash and Linda Reynolds.

AEC spokesman Phil Diak said there was nothing to suggest an "untoward removal" of the ballot papers.

Special Minister of State Michael Ronaldson did not think it was an "issue of skulduggery", but said it was a disturbing development which required an inquiry.

Independent senator Nick Xenophon thinks there should be a fresh election in WA if the ballot papers cannot be found.

"Better to cost money now than have a result where there is a question mark over those that have been elected," he said.

Opposition Leader Bill Shorten said WA deserved an explanation and while there was a way to go with due processes, another election could not be ruled out.

"This is a very serious matter," he said in Canberra.