The federal agency responsible for worker safety and other protections for tens of millions of Americans has failed for decades to establish a system to shield whistleblowers from retaliation from their employers, according to government auditors.

The Government Accountability Office’s report criticizes the Labor Department’s Occupational Safety and Health Administration for “ineffective” whistleblower protections that have persisted 20 years after auditors first reported weaknesses.

The stakes have only grown for workers and the public over the last decade, as OSHA – created to ensure safe and healthy working conditions for employees – has expanded its mission. The agency is now charged with enforcing 18 whistleblower laws, covering private employers in the areas of nuclear power, transportation, securities, consumer product safety and the environment.

“For over 20 years, we have repeatedly found that [the agency] lacks sufficient internal controls to ensure that standards for investigating whistleblower complaints are consistently followed,” the 46-page GAO report, released last week, concludes.

Auditors described “significant internal control problems” in the whistleblower protection program, adding, “The problems appear systemic, and sustained management attention is needed to address them.”

Workers who report on waste, fraud or other prohibited or unlawful practices in the workplace can play a crucial role in making sure federal laws are enforced. But whistleblowers risk reprisals from their employers, including demotion, reassignment and firing, auditors said. Federal laws establish a process for workers who believe they have faced retaliation to report their concerns to investigators.

As President Obama took office in January 2009, auditors conducting one in a long line of reviews of the whistleblower program reported that OSHA investigative teams were short-staffed and lacked adequate training and resources to do their jobs. The investigators also had insufficient oversight by superiors to ensure that complaints were properly investigated. The GAO recommended changes to address the problems.

When auditors returned a year later, most of the problems remained. While some regional offices took whistleblower complaints more seriously than others, many investigators still lacked formal training. The agency’s national headquarters lacked accurate files and data to ensure that a case brought to regional office was investigated.

The program is also not routinely audited, and audits that were performed “lacked independence,” auditors found.

OSHA has hired 25 new investigators this year, but the process of assigning them to regional offices was “not transparent” – some areas of the country are underrepresented, with a high number of complaints awaiting investigation.Money for the whistleblower program is often not tracked separately from OSHA’s general budget, auditors found.

Asked Tuesday why the problems have lingered for two decades, OSHA spokesman Jason Surbey cited a “lack of resources” and said the agency is conducting a “top to bottom” review of the whistleblower program – even though numerous reviews have been done over the years.

“The agency is working hard to ensure that whistleblowers are protected from retaliation,” Surbey said in a statement. “The objective is to identify any weaknesses and inefficiencies in the program and improve the ways it conducts this very important activity.”

OSHA’s director, David Michaels, has been on the job just nine months.

The GAO report comes as efforts heat up in Congress to strengthen whistleblower protections across government. The House has twice passed legislation that would give federal employees the right to sue agencies that retaliate against them for exposing improper actions or policies. Opposition in the Senate to applying such a provision to national security workers is under negotiation.

The new financial regulatory law contains a provision offering cash rewards to individuals who report violations of securities law, while the new health-care law offers protections to caregivers or medical staff who challenge breakdowns in patient safety or denials of coverage by insurance companies.

The Center for Public Integrity reported in July that since 2002, when Congress passed the Sarbanes-Oxley corporate reform law, the Labor Department tossed out 1,066 whistleblower claims of corporate fraud and upheld 25 claims. Michaels said then that he had ordered a review of the agency’s handling of those cases and other whistleblower statutes.

“OSHA failed to deliver on nearly all the commitments made by the Obama administration for so many corporate whistleblowers,” said Tom Devine, a whistleblower advocate and legal director of the Government Accountability Project. “We hope the [report] will be a healthy wind at the back of those toiling inside the agency.”