If Investigations Commissioner Mark Peters is actively investigating political interference in the Department of Education’s “probe” into Jewish religious schools that don’t actually teach their students, then City Hall needs to let him do his job.

Mayor Bill de Blasio’s minions suggest Peters is making barely veiled threats to avoid getting fired. But if, as The New York Times reports, Peters is on the yeshiva-DOE case, City Hall should back down.

In a letter last week to First Deputy Mayor Dean Fuleihan, Peters cited “matters now being pursued by DOI in which the mayor himself, and/or his staff, are potentially a subject of investigation.”

It’s believed he was referring to a DOE farce of an investigation into some ultra-Orthodox yeshivas that allegedly fail to provide adequate non-religious instruction.

After two long years, DOE reported that it had examined only a third of the target schools, all of which it said had “passed.”

But this probe reeked of politics from the outset: This year, the politically potent ultra-Orthodox Jewish community got the Legislature to water down state requirements. And de Blasio has long enjoyed a close relationship with the community.

Peters wouldn’t confirm just what he was referring to but told the Times: “If they believed this was solely a reference to any investigation involving yeshivas, that belief would be wrong.”

Clearly, Peters is trying to regain the offensive after an inquiry determined he’d abused his power in one matter. But he has also exposed significant scandals at NYCHA, the Administration for Children’s Services and the mayor’s Office for Contract Services. De Blasio, needless to say, is not happy.

All the more reason why City Hall should keep its hands off, especially in a matter already so politically tainted as the yeshiva probe. Peters has proved himself; the mayor, much less so.