The city’s Board of Elections suspended the top official at its Brooklyn office without pay as they probe the mysterious purge of more than 120,000 Democratic voters from the borough rolls that wreaked havoc on Tuesday presidential primaries.

The solo suspension of Diane Haslett-Rudiano from her $125,000-a-year post over widespread polling problems is raising eyebrows that extend beyond party lines.

Democrat Betty Ann Canizio, the BOE Deputy Clerk for Brooklyn, is the official primarily responsible for overseeing the borough’s Democratic voting rolls while Haslett-Rudiano, a Republican, oversees her party’s rolls, sources said.

“It sounds like they cut a deal to make the Republican the scapegoat and protect Betty Ann,” said an elected Brooklyn official who’s a Democrat.

Canizio is an ally of Brooklyn Democratic Chairman Frank Seddio. She has a long history as a borough district leader of rubber-stamping his candidate nominations and political appointments. Seddio used his political muscle to help Canizio, 68, secure her $120,000-a-year post, sources said.

BOE sources say she’s routinely absent or works half days. She failed to show up for work Thursday and wasn’t at her Bay Ridge home when visited by a Post reporter.

Canizio was also at the center of a illegal parking placard scandal that rocked her office — yet somehow avoided punishment.

Two Brooklyn elected officials told The Post Canizio bragged at a Democratic committee meeting in 2014 that she illegally gave away her city-issued parking placard to her husband so he could avoid tickets. She then recruited David Annarummo, a BOE administrative associate, to drive her to and from work as part of his duties.

Annarummo was one of the five staffers busted using fake, photocopied parking placards and slapped with fines of up to $500 by the city’s Conflicts of Interest Board.

He signed a disposition last September admitting to using a “forged” permit to drive his boss to work from June to December of 2014. His statement never mentioned Canizio by name but notes “the deputy chief clerk was in the vehicle while the forged BOE parking permit was displayed in the windshield. For this reason, I believed that the heads of the BOE Brooklyn Borough Office were aware of and condoned employees’ use of the forged parking permits.”

The COIB only three weeks ago fined Sheila Del Giorno, chief clerk at the BOE’s Staten Island location, $3,500 for also grubbing car-pool rides from co-workers without compensation –which is a violation of city rules. Unlike Canizio’s free rides, none of the Staten Island workers who drove Del Giorno around from 2007 to 2015 were found using fake placards.

“It’s an utter disgrace that Betty Ann got off without even a slap on the wrist from the Conflicts of Interest Board, considering she was well aware the fake placards were being photocopied and distributed like candy at her office,” said one Brooklyn politician.

The internal investigation by BOE comes after state Attorney General Eric Schneiderman and City Comptroller Scott Stringer already announced they’re investigating widespread complaints from voters at polling sites citywide during Tuesday’s primaries.

When reached by phone, Halsett-Rudiano and Canizio declined comment.

The COIB also declined comment.

BOE Executive Director Michael Ryan said “we don’t comment on personnel matters” when asked why Canizio has yet to be reprimanded.

Meanwhile, Canizio is currently snubbing election law. She is a longtime district leader representing Bensonhurst but recently moved to Bay Ridge. She plans to run for district leader in Bay Ridge in September.