Hands off.

An explosive whistleblower complaint sent to three city councilmen claims the agency charged with investigating wrongdoing in city schools has blocked probes of Mayor Bill de Blasio, Schools Chancellor Richard Carranza and their allies, The Post has learned.

The Special Commissioner of Investigation (SCI) for city schools is sitting on nine cases of waste, fraud and corruption involving the upper echelons of City Hall and the Department of Education, according to a type-written, four-page letter that catalogues the wrongdoing in detail.

One of cases cited involves first lady Chirlane McCray’s embattled $850 million mental health program, Thrive, which has a large school component.

The insider document blames Special Commissioner Anastasia Coleman, who was appointed in February 2018, after prevailing in a power struggle with former Department of Investigations Commissioner Mark Peters, an aggressive prober of the mayor’s administration and city agencies.

“Under Coleman, SCI is continuing to hold or redirect investigations into City Hall, Chancellor Richard Carranza and de Blasio allies with business or that are connected to the DOE to protect de Blasio’s image while he runs for president,” says the anonymous Aug. 20 letter signed by “SCI Investigative Staff.”

De Blasio dropped out of the presidential campaign on Sept. 20.

Other mothballed cases included a probe of possible mayoral interference in an investigation of Orthodox Jewish yeshivas that get city funds but skimp on required secular education; contract spending on de Blasio’s aborted “Renewal” program for failing schools; and allegations about Carranza and his top aides.

“SCI investigators assigned to investigations involving executives at the DOE and City Hall, including the Mayor, have been directed to instead focus on matters not related to the mayoral administration, his allies, etc,” the letter says.

SCI agents, it adds, “have been denied support in conducting these investigations and their independence in pursuing leads . . . that point towards City Hall and top-level executives at the DOE.”

In response, SCI said that Coleman “is aware of the anonymous complaint as well as its recipients,” adding that the letter was forwarded “to the appropriate agency for review” — referring to the city Department of Investigation.

Coleman denied the accusation her office has protected the powerful. The statement says, “the Commissioner added, unequivocally, that SCI has not, and will never, slow-walk an investigation based on the subject or the subject matter of the complaint.”

Jane Meyer, a spokeswoman for the mayor, said, “Any Implication that City Hall directed SCI to slow walk Investigations is untrue and ridiculous. We respect the Special Commissioner of Investigation’s independent authority.”

Coleman was at the center of a battle between City Hall and former DOI chief Peters. In February 2018, Peters tried to seize control of SCI. He fired Coleman after she reportedly resisted his attempts to have more say over SCI investigations. That led de Blasio to issue an executive order giving only the mayor power to hire or fire SCI commissioners.

The mayor canned Peters, a former close friend and campaign treasurer, in October 2018, after a series of damning DOI probes of city agencies, including major problems at the Administration for Children’s Services following a toddler’s death.

In a letter after his ouster, Peters accused Hizzoner of axing him in retribution for past probes and to stem ongoing investigations. Peters said the mayor had screamed at him in a late-night call, accused him of trying to bring his administration “down,” and demanded he keep the January 2017 ACS report under wraps.

The recent incriminating missive was sent to City Council members Ritchie Torres, chairman of the oversight and investigations committee; Mark Treyger, chairman of the education committee, and Robert Holden, who has called for a federal RICO investigation of academic fraud in city schools.

Holden said he forwarded the letter to the Queens District Attorney’s office, which is overseeing a probe of grade-fixing at Maspeth High School.

Both Torres and Treyger told The Post the letter raised red flags they have already recognized.

“The letter confirms what we’ve long known: The SCI, as constituted, appears fundamentally ineffective at overseeing the DOE,” Torres said. “The overseer needs oversight of its own.”

He added: “It’s strange that the DOE — the behemoth of city government — is subject to the least amount of oversight.”

The DOE’s $34 billion budget makes up about a third of all city spending.

Treyger agreed: “The largest department in the city of New York deserves a robust watchdog that can effectively do its job.”

Torres and Treyger have met with Coleman and stressed the need for SCI to conduct pro-active, systemic investigations of the DOE, and offered to help with funding if needed.

Since then, the SCI issued a review of the DOE’s training to combat student-to-student sexual harassment. In September, SCI issued a blistering report finding that the DOE paid nearly $9 million for 6,000 school-bus GPS units while up to 80 percent were never turned on. The bungling also prevented the city from obtaining Medicaid reimbursements for special-ed services.

But the SCI has punted on academic misconduct. The agency received 880 complaints of test-tampering and grade fraud in the past three years, but sent 823 to the DOE to investigate itself. The DOE won’t give the results.

On the yeshiva issue, frustration has plagued Naftuli Moster, executive director of YAFFED, an advocacy group that triggered the DOE’s investigation in July 2015. Still waiting for the probe’s completion, Moster has long suspected the mayor’s office made DOE drag its feet to pander to Orthodox Jewish leaders.

“Now it appears the investigation into possible mayoral interference is also being stonewalled,” Moster said. “We need to get to the bottom of this.”

Torres complained that SCI has ignored big issues.

“The NYCHA inspector general had a leading role in exposing the lead crisis in public housing. By contrast, SCI had no role at all in exposing the lead in city schools,” Torres said.

“SCI is MIA.”