A city agency that investigates school employee misconduct has probed only about 1 percent of the hundreds of cheating allegations it received.

The office of the special commissioner of investigation for city schools, Richard Condon, conducted three probes into alleged test tampering and grade changing — out of about 300 complaints — in 2014.

The number of open cheating investigations this year rose to four — again out of about 300 complaints.

Cheating allegations made up nearly 6 percent of all complaints Condon’s office reviewed in 2014, spokeswoman Regina Romain said.

Instead of probing the allegations of academic fraud, the SCI passed most along to the city Department of Education’s investigative unit, the Office of Special Investigations. The SCI operates under the city Department of Investigation and is independent of the DOE.

The SCI’s referral of the allegations put the DOE in the convenient position of investigating itself, critics say.

“It’s important that investigators are seen as independent, have professional expertise, and have no vested interest,” said Rob Brenner, a former deputy commissioner at the SCI who authored a 1999 report on cheating in schools. “Witnesses who are likely to be other school employees will be pretty wary about coming forward to an internal DOE entity.”

The SCI’s probers, many of whom are retired NYPD detectives, seem better equipped to get to the bottom of fraud than those at the OSI, who are more likely to be lawyers, experts said.

“It feels like a police inquiry” when the SCI is involved, said Columbia University education professor Eric Nadelstern.

Romain and DOE spokesman Harry Hartfield refused to say exactly how many academic-fraud complaints the SCI referred to the OSI, or how many of the complaints were substantiated.

“There is zero tolerance for schools that don’t adhere to our academic policies, and we are committed to ensuring that we have the staff needed to investigate any allegation of misconduct,” Hartfield said, referring to the OSI’s capabilities.

But critics blasted Condon’s office for brushing off cheating cases.

“They hang onto the sexier cases and pass off everything else to OSI,” Nadelstern said. “Test tampering does not meet their criteria for one reason or another.

“In a situation where there appears to be widespread cheating in the schools, nobody connected to the Department of Education, SCI, City Hall, or the state Department of Education looks good. It appears they aren’t being vigilant enough.”

The de Blasio administration has come under fire for a grade-fixing scandal that has raised questions about the value of city high-school diplomas.

Insiders say Mayor de Blasio and DOI Commissioner Mark Peters — who oversees Condon — have shifted the priorities of the city’s main investigative agency away from schools.

Instead, Peters has directed resources toward jail corruption and day-care operators, because de Blasio wanted to clean up Rikers Island and launch a universal pre-K program, said a source familiar with the DOI.

“It did often occur to me why more [academic fraud] isn’t being investigated,” the source said. “If somebody is defrauding to make stats look good or cover up nonperformance, I wouldn’t see why you wouldn’t look into that.”

After Post exposés this summer about cheating school administrators, Schools Chancellor Carmen Fariña last week said she would form a $5 million task force of city DOE administrators to look for irregularities in exam scores, credits or graduation rates, and turn them over to the SCI.

But critics said an independent body should monitor the school system for cheating.

“You can’t audit yourself. That’s Accounting 101,” said state Sen. Simcha Felder (D-Brooklyn), chair of the Senate Committee on Cities, which oversees city schools.

Additional reporting by Susan Edelman and Carl Campanile