Australian Electoral Commissioner Ed Killesteyn says there is "a nagging and almost irreconcilable doubt" about the outcome of the West Australian Senate election.
But he says the AEC is legally obliged to declare a result, which it will do at midday (WST) on Monday.
This is despite the commission revealing last week that 1375 ballot papers had gone missing between the initial count and the recount.
"This is very damaging to the reputation of the AEC which has been earned over many, many decades of dedicated service to the Australian community," Mr Killesteyn told ABC radio on Monday.
"We're left with a nagging and almost irreconcilable doubt about the outcome of the West Australian Senate election."
FRESH ELECTION SHOULD BE HELD SOON: TRUSS
Deputy Prime Minister Warren Truss says any fresh Senate election in Western Australia should be held as
soon as possible.
Mr Truss says a new poll would certainly carry many of the characteristics of a by-election.
"If there is a new election and that will be a matter for the courts to decide, it needs to happen as quickly as possible," he told ABC television on Sunday.
Greens senator Scott Ludlam says he allowed himself a brief moment of celebration on being declared
re-elected but he's not sure it will stick.
Senator Ludlam says he completely understands why the result of the West Australian senate recount is likely to be appealed.
But he had to wait eight weeks since the September 7 election to finally be declared a winner on Saturday.
"So I did allow myself a moment of celebration," he told ABC television on Sunday.
"I am not really sure that the win will stick. At least two parties that I am aware of have already said they will take it to the Court of Disputed Returns. To be perfectly honest that's probably what I would have done as well."
Senator Ludlam said the Greens' position was that former Australian Federal Police commissioner Mick Keelty should have been given time to find 1375 votes that were controversially lost by the Australian Electoral Commission (AEC).
On Saturday, Palmer United Party leader Clive Palmer said he would challenge the election of The Greens' Scott Ludlam and the Australian Sports Party's Wayne Dropulich to the Senate in a controversial partial recount in Western Australia
Mr Palmer said he would go to the High Court with the case after his candidate Zhenya "Dio" Wang and Labor's Louise Pratt missed out despite having been successful in the initial count.
Mr Palmer is unhappy that the recount didn't include 1375 votes that were lost by the Australian Electoral Commission (AEC).
The lost votes from electorates of Pearce and Forrest prompted an investigation by former Australian Federal Police commissioner Mike Keelty and Mr Palmer wants the outcome of the first count upheld.
"If this is not done, we believe the only fair outcome is a new election with all senate positions declared vacant," Mr Palmer said.
"The original count should stand as that is the only count where we've had a full count of all votes."
Labor would also appeal, the ABC reported.
The court, sitting as the Court of Disputed Returns, will decide whether a by-election should be held.
The AEC ordered the partial recount on October 10 because the close result for the sixth Senate seat led to appeals by the Greens and Australian Sports Party. Senator Ludlam initially lost out by the wafer-thin margin of 14 votes.
He argued that it was important that the votes were scrutinised so human error could be ruled out, noting the AEC had a policy of automatically recounting for the House of Representatives where the difference between candidates was less than 100 votes.
Senator Ludlam said he was delighted with the recount result, but acknowledged the matter wasn't yet settled.
"We know of course that other parties are likely to take a very close look at the numbers," he said.
"Hopefully this allows us to get on with our jobs with a degree of certainty but I'm also well aware that there could be a few twists and turns in this yet."
Mr Dropulich, who had requested a full recount, said he was very excited by the result.
"Obviously there's still some more things to be worked through for the AEC ... so we'll wait and see what's going to happen," he said.
"It's still a waiting game at this stage."
Liberals David Johnston, Michaelia Cash and Linda Reynolds, and Labor's Joe Bullock, who were victorious in the initial count, held their seats after the recount.
Senator Ludlam said on Twitter that he believes the margin in the partial recount was just 12 votes.
The results will be formally declared on Monday at 12pm (WST) then a writ will be returned to the WA Governor Malcolm McCusker.
Candidates and the AEC will then have 40 days to appeal to the Court of Disputed Returns.
Senator Ludlam said on Twitter that he believes the margin in the partial recount was just 12 votes.
The results will be formally declared on Monday at 12pm (WST) then a writ will be returned to the WA Governor Malcolm McCusker.
Candidates and the AEC will then have 40 days to appeal to the Court of Disputed Returns.
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