New York City Comptroller Scott Stringer said Tuesday that he will audit the local Board of Elections over “polling problems” and “widespread reports of voter disenfranchisement” during the presidential primaries.

In a letter to the board’s executive director, Michael Ryan, Stringer said his office would probe the agency’s operations “to identify failings and make recommendations” after Tuesday’s presidential primaries and several local races.

“We’re going to go in and ask some very tough questions,” Stringer, a Democrat, said at a news conference in lower Manhattan.

In a prepared statement, Mayor Bill de Blasio said he supported Stringer’s probe. De Blasio said the allegations of irregularities in Tuesday’s elections undermine “the integrity of the entire electoral process and must be fixed.”

De Blasio said he wants the elections board to undo a reported voter purge in Brooklyn by relying on citywide, rather than borough-based, voter rolls.

Among problems reported Tuesday to city and state authorities were that 125,000 people were removed from the voter rolls; 60,000 people received notices that omitted the primary’s date; and that prospective voters found polling sites closed during hours the sites should have been legally open.

Board of Elections spokeswoman Valerie Vazquez did not return a voicemail message Tuesday seeking comment.

The Board of Elections, which is run by a bipartisan board of appointed by the two major political parties, has long been criticized.

A probe three years ago done by the Department of Investigation under former Mayor Michael Bloomberg found nepotism, inadequate constraints against voter fraud and undue political influence at the board. Among the findings were that staffers helped family members get promotions or jobs, and that undercover investigators were permitted to vote while using the names of felons, out-of-state voters or the deceased.

“There’s no other agency like the board of elections in the world or in the United States where politicians from both parties come together and run an agency like it’s a backroom Tammany Hall political club,” Stringer said Tuesday.

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The state attorney general’s office said that by 4 p.m. Tuesday, it had received 562 telephone calls and 140 emails with complaints from voters across New York. That compared with a total of 150 complaints for the 2012 general election, said Nick Benson, spokesman for Attorney General Eric Schneiderman.

“The most common complaint has been from individuals who attempted to vote but were told that they are not registered to vote whatsoever,” Benson said. “The second most common complaint has been from individuals who are registered, but have been informed that they are not registered with a particular political party and may not participate in the partisan primary of their choice.”

With Yancey Roy