The battle in the final federal electorate of Herbert could end up in court, Prime Minister Malcolm Turnbull believes.
Labor's Cathy O'Toole leads sitting Liberal MP Ewen Jones in a recount by 35 votes, amid allegations defence force members weren't able to cast their ballots.
"There may well be a challenge to it because there are allegations people were not able to vote," Mr Turnbull told 2GB radio on Thursday.
Mr Turnbull, who visited the Lavarack Barracks in Townsville on Tuesday, said there was "real concern and real disappointment" about the allegations.
"It is absolutely critical that every Australian has the opportunity to vote," he said.
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Australia's compulsory voting system was a "two-way street" and the electoral commission owed it to voters to make sure they can cast their ballots.
"These are all matters which could well be the subject of a hearing in the Court of Disputed Returns," he said.
Mr Turnbull would not say whether the Liberal Party would pursue the case in court.
"Obviously the party will look at the evidence and assuming the final vote were to be adverse, form a view about whether to make an application to the court."
Liberal senator Ian Macdonald, who has been scrutineering the count, says informal votes and votes put in the wrong pile are still being discovered.
But the full count of preferences would help ensure every allocation had gone in the right column.
"It's been a torturous process," he told ABC radio.
There was a number of irregularities in the votes accepted and rejected, with several people complaining they weren't able to vote, he said.
A by-election would be triggered should the Court of Disputed Returns overturn a Labor victory.
