The final result in the federal seat of Herbert appears likely to end up in court after a series of problems.
Special Minister of State Scott Ryan will ask the electoral commission for a briefing on why defence personnel might have been denied a vote at the election.
Sky News reported on Thursday soldiers from Townsville, on which Herbert is based, who were involved in a military exercise in South Australia during the election campaign may have missed out on a vote.
More than 600 soldiers who were participating in Exercise Hamel are understood to have been unable to vote, including 543 from the 1st brigade based in Darwin and Adelaide.
But 85 others, including some from Townsville, may have also missed out.
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A full recount is under way in Herbert after the initial count ended with a margin of only eight votes in Labor's favour.
Anything under 100 votes triggers an automatic recount.
Senator Ryan, who took on his new role this week, said the Australian Electoral Commission went to a lot of trouble to ensure people who were travelling interstate and overseas did not miss out on voting in their home electorates.
He said it "raises a concern" if anyone can't vote.
"It's one of the things I will chase up with the commission," Senator Ryan told Sky on Thursday.
But he said he would wait until after the recount and the final Senate count.
Sky said Defence had refused to say where the 85 mystery soldiers are based.
But it is understood Townsville-based soldiers were involved in Exercise Hamel.
There have also been reports of Herbert ballot papers being unavailable for absentee voters in the north Queensland seat of Kennedy.
Herbert is the final seat to be determined.
If the coalition can retain it, Prime Minister Malcolm Turnbull will have 77 seats in the 150-seat parliament allowing the government to appoint a speaker while retaining an absolute majority.
The AEC said it was aware of the report.
"The AEC worked with the ADF during recent exercises to provide voting services," it said in a statement.
