The Defense Department has inadequately protected from reprisals whistleblowers who have reported wrongdoing, according to an internal Pentagon report, and critics are calling for action to be taken against those who have been negligent.

The report, dated May 2011, accuses the officials, who work in the Defense Department’s Office of Inspector General, of persistent sloppiness and a systematic disregard for Pentagon rules meant to protect those who report fraud, abuses and the waste of taxpayer funds, according to a previously undisclosed copy. The report was obtained by the Project on Government Oversight, a nonprofit watchdog group.

A three-person team of investigators, assigned to review the performance of the Directorate for Military Reprisal Investigations, concluded that in 2010, the directorate repeatedly turned aside evidence of serious punishments inflicted on those who had complained.

The actions included threatened or actual discharges, demotions, firings, prosecutions and a mental health referral. At least one of the alleged reprisals was taken because the complainer had written to Congress, an act that Pentagon regulations say is a “protected communication” immune from retaliation. Some of the other whistleblowers had alleged discrimination, travel violations and “criminality,” the report states.

In all, investigators disputed the directorate’s dismissal of more than half of the 152 whistleblowing cases it reviewed and called for it to revamp its procedures and start enforcing the protective rules.

Sen. Charles E. Grassley (R-Iowa), the Senate Judiciary Committee’s top Republican, called the report disturbing. “Heads must roll,” he said in an April 24 letter to Lynne M. Halbrooks, acting inspector general. “The root cause problems identified in the report must be addressed and resolved immediately.”

Halbrooks responded in an April 26 letter to Grassley that the reprisal investigations office now has new leadership but added that “I strongly disagree with the assertion” that IG officials knowingly ignored the law. “I stand behind the continued professionalism and dedication of our reprisal investigators, past and present,” she said.

The creation of the reprisal investigations unit grew out of hearings and legislation in the 1990s that spotlighted the military’s practice of ordering mental health evaluations for whistleblowers, a move that hindered their careers. The office, which is expanding this year from 31 to 51 employees, is responsible for investigating complaints of retaliation by troops and Pentagon employees and for overseeing such probes within the military services.

Under federal law, prohibited reprisals are adverse actions taken in response to protected disclosures, which involve reports of violations of laws or regulations, gross mismanagement, abuses of authority, and dangers to health and safety.

Report prompted changes

In response to the report, the Defense Department’s deputy inspector general for administrative investigations, Marguerite C. Garrison, last year reorganized the office and began an overhaul of its manual.