The Department of Education launched an audit yesterday to investigate the missing financial reports of a Lower East Side school’s Parent Teacher Association that resigned last week to protest the new principal.

The audit has aggravated an ongoing conflict between the Department of Education and the parents’ group, which claims it has documented the reporting of its finances each year. The PTA claims the audit is retaliation for criticism of the school’s administration.

Two investigators in long black trench coats hovered outside the PTA office at the New Explorations Into Science, Technology and Math School yesterday, waiting for the parents to sort and copy all of the organization’s documents. After an argument broke out as parents sat down to a lunch break, one investigator yelled that the parents “have a bad attitude.” The parents shot back, calling the investigators bullies.

“It’s such harassment. It’s on a level I never thought possible,” the PTA president, Emily Armstrong, who was among nine PTA officers that resigned last week, said. “They’re not supposed to barge in here like this.”

A Department of Education spokeswoman, Kelly Devers Franklin, said the audit was triggered several months ago when the incoming NEST+m principal searched for the school’s PTA financial reports for the past two years and couldn’t find them. She said auditors tried, and failed, to schedule a meeting with the PTA’s lawyer two weeks ago. The PTA confirmed this, saying its lawyer is currently out of the country. When the PTA resigned abruptly last week, Ms. Devers Franklin said a special investigator had also been brought in to oversee the audit.

Audits of PTAs are routine, Ms. Devers Franklin said. “It’s completely ridiculous that it would be retaliation,” she said.

The PTA officers resigned during a raucous meeting last Thursday that ended when an assistant principal called police to eject parents from the building. The officers said they resigned because they disagreed with changes made by the new principal, Olga Livanis, who was appointed after a bitter fight last year over Department of Education plans to install a new charter school inside the NEST+m building.

The PTA filed a lawsuit last year to keep the charter school out, but the suit was dropped when the city decided to put the charter school elsewhere.