One of the Big Apple’s most lauded restaurants is eating crow at the city’s Health Department.

Per Se, the three-Michelin-starred eatery in the Time Warner Center, lost its “A” rating last month after city inspectors wrote up seven violations and slapped it with a not-so-stellar “Grade Pending.”

Five of the violations were deemed “critical” by inspectors.

They included no hand-washing facility in the food-prep area, hot food held below 140 degrees, cold food held over 41 degrees, eating or drinking in the food-prep area and tobacco use.

The 42 violation points are enough to knock Per Se’s grade to a dreaded “C” if it doesn’t clean up its act before a follow-up review.

The slap is going to shock the restaurant’s many fans, who rave on Yelp that it’s “astounding,” “perfect in every way” and “My Holy Grail.”

According to city records, Per Se — where a prix-fixe dinner for two goes for $620 before tax and tip — has received more than 40 violation points on three occasions.

Each time, it has aced the follow-up and for a final “A.”

Reps for Per Se owner Thomas Keller did not respond to phone or e-mail requests for comment.

In 2012, The Post reported that Per Se avoided having to post a subpar grade thanks to a well-placed call to the Health Department.

The call came after an inspector hit the restaurant with violations totaling 22 points.

That meant Per Se was facing a “B,” a grade hardly in keeping with its astronomical price point.

Officials accepted Per Se’s explanation that an inspector had made a mistake and downgraded the violations so the eatery could post an “A” grade.

At the time, a Health Department spokesman insisted that Per Se didn’t get special attention and that any eatery could call and challenge its mark.

But owners of other restaurants insisted they got nowhere trying to solve grade disputes by phone.