A Long Island school clerk overseeing board of education elections tore up ballots and threw them in a dumpster to help her favorite candidate win, a newly revealed internal probe found.

Hempstead Union Free School District Clerk April Keys allegedly rigged the May 19 trustee election by smuggling official ballots out of her office and handing absentee ballots to favored candidate Victor Pratt so he could trash them, according to a 51-page petition filed by the district with the state Education Department.

Keys could now face criminal charges as the district is looking to overturn Pratt’s razor-thin win.

“The Board of Education Trustee election must be overturned because widespread irregularities affected the outcome of the election and were so pervasive that they vitiated the electoral process,” the filing, from the Hempstead school district’s attorneys, said.

The filing, which was submitted June 15 but emerged Thursday,  asks state Education Department Commissioner Betty Rosa to order a new one election, with a replacement clerk and oversight by the state Attorney General’s Civil Rights office.

Question marks were first raised by the district after it discovered major irregularities in its election.

Pratt won by just 81 votes — boosted by a suspiciously large number of absentee and early mail ballots that boosted him to the win even though he only came in third on machine voting, the probe found.

Pratt racked up 87% of absentee votes and 55% of early mail votes, compared to just 27% of in-person machine votes – while other trustee candidates received fewer than 100 absentee and early mail ballots combined, the probe found.