Nassau, Suffolk and Queens election boards have sent out military absentee ballots for a court-ordered Oct. 6 GOP primary in the 3rd Congressional District and state election officials also are seeking a federal waiver because a late primary date would prevent military absentees from going out 45 days before the general election in November as required.

The move on Monday to send out ballots early satisfies the 45-day rule for the new primary to protect military votes, but leaves unclear the impact on the general election should the federal waiver be denied.

The latest twist in the topsy-turvy contest comes after U.S. District Court Justice Frederick Scullin in Syracuse last week ruled in favor of a new primary date sought by Republican challenger Philip Pidot in his battle with GOP designee state Sen. Jack Martins. That decision came after state courts found Pidot had more than the 1,250 signatures needed to qualify for the primary, but there was not enough time to include the race on New York’s June 28 congressional primary.

Scullin also ordered state election officials to apply for a general election waiver from the Federal Voting Assistance Program, because there will be only 33 days between the new primary date and the Nov. 8 general election.

Under program guidelines, a state can get a waiver due to a “legal contest,” but must show there is an “undue hardship” that is “so severe that integrity of the election for federal office and the rights of all of a state’s voters to participate in that election is threatened.” A state also must show it has a comprehensive plan that makes up for the shortened period and gives military voters more than one method of electronic or other expedited way to return ballots.

In their waiver request, state election officials said they would certify the Oct. 6 primary as early as the next day if the results are not close, use express mail to send out ballots and extend the deadline for military voters and civilians who live overseas to send back their ballots until Nov. 29.

Scott Wiedmann, FVAP spokesman, said five of 11 waivers sought were granted in 2010 when the 45-day requirement was first imposed. Since then, there have been only two requests, one from New York in 2012 and another from West Virginia in 2014 — both of which were denied. Wiedmann said a decision will be made by Monday.

In all, there are only 246 military and overseas absentees that could play a role in the Oct. 6 GOP primary. State election officials say there are 1,012 military and absentee ballots that could be affected in the general election.

Nicholas LaLota, Suffolk’s Republican election commissioner, in an email criticized the state board for failing to ask the federal court to consider the state primary date of Sept. 13 for the congressional primary, saying it would save taxpayers money and has the potential for less impact on military voters.

While state officials also would need a 45-day waiver to hold the GOP primary Sept. 13, he said there are only 22 Suffolk military absentees for that contest. With a normal turnout of about 10 percent, he said as few as two voters might be affected. In the general election, where there are 169 Suffolk military and overseas absentees, LaLota said 85 military voters could be disenfranchised.

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For Suffolk, LaLota added that the extra cost of the Oct. 6 congressional primary would be $350,000 for inspectors and setup. He had no figures for Nassau or Queens, but noted Suffolk only makes up about one-third of the congressional district.

Meanwhile, Scullin has set Oct. 30 for oral arguments on Martins’ bid to get a new Dec. 6 date for the general election, or withdraw the order for the Oct. 6 primary.