When Kathleen Elvin took over troubled John Dewey High School in March 2012, she had a mandate to turn it around. And by at least one measure, she pulled off the job in barely two years.

But Dewey’s soaring graduation rates, which increased 13 points under Elvin, were bolstered by an illicit credit recovery program, a city investigation has found. A long-awaited report on the probe, released Wednesday by the city’s Office of Special Investigations, concluded that Elvin supervised the set-up, in which students received credits toward graduation with no instruction from teachers.

It is the first major probe of academic fraud to come to light under Chancellor Carmen Fariña, who downplayed the allegations weeks ago after they surfaced in news reports in March. On Wednesday, Fariña said in a statement that the city was acting swiftly in response to the report’s findings, which she called “disturbing.”

“We have begun the process to have Ms. Elvin’s employment terminated, and she will be removed from payroll shortly,” Fariña said in a statement. Officials said principals and superintendents would receive a training session this summer to ensure they were not violating the city’s policies for high school credit accumulation.

Those policies were established in response to growing concerns that “credit recovery” courses were being abused to inflate graduation rates, which factor heavily into evaluations of struggling schools. Those programs allow students to make up failed or incomplete classes without having to repeat entire courses, often through online assignments or packets of worksheets that teachers are supposed to supervise.

Starting with the 2013-14 school year, the city capped the number of credits students could earn through credit-recovery programs and put new restrictions on when students were eligible to make up work, and provided high school principals with clearer guidance about graduation requirements.

But Elvin did not follow the new protocol at John Dewey that year, according to the probe, which began in April 2014 in response to complaints from the school’s teachers. They reported that Elvin and assistant principals pressured teachers to give students credits for courses that they had either failed or did not take, regardless of effort or performance. When teachers refused, administrators changed grades themselves.

Alan Lerner, a social studies teacher, told investigators that two students who failed his Participation in Government class last spring had their grades changed to passing, unbeknownst to him. Another teacher assigned to a “Project Graduation” course, one of the credit recovery programs overseen by Elvin, reported that students who showed up to class and completed the work were automatically given a passing grade.

The report marks the end of a saga that began when the Bloomberg administration tapped John Dewey and 32 other schools for a federally prescribed “turnaround” in 2012 and appointed Elvin to lead the effort. The plans, which required principals to remove half of the school’s teachers, were later blocked through legal action. Elvin stayed on at John Dewey, but clashed with staff members who resented her aggressive tactics for removing teachers.

Martin Haber, a special education teacher who said he was forced into an early retirement last year after more than 20 years at the school, described the tension in dramatic terms.

“This principal created a hostile work environment where teachers were being slaughtered,” said Haber.

But when the city’s graduation rates were released at the end of each year Elvin was there, John Dewey showed improvement. Before she took over, 66 percent of students graduated in four years; last year, 79 percent of students did.

“It didn’t seem possible,” Haber said of the growth.

Fariña’s decision to bring termination charges against Elvin is harsher than the Bloomberg administration’s treatment of Janet Saraceno, the principal of Lehman High School who investigators found guilty of similar kinds of academic malpractice in 2011. Saraceno resigned voluntarily and took an administrative position with the department coaching principals and teachers.

Representatives for the United Federation of Teachers and the Council of Supervisors and Administrators, the union that represents Elvin, did not respond to emails seeking comment.

Norm Scott, an activist with the Movement of Rank and File Educators, a caucus of the city teachers union that waged a public campaign to remove Elvin, said the city’s actions were long overdue. He said Fariña — who has said for months that she was awaiting the results of the investigation — was informed about problems at John Dewey by teachers there in her first months on the job.

“A year too late,” Scott said. “Kids and teachers have suffered enormously.”