Auditors for two federal agencies are examining the operations of Arlington-based International Relief and Development, a nonprofit organization that is the largest recipient of grants from the U.S. Agency for International Development. The vast majority of its funding — 82 percent of $2.4 billion — went to projects in Iraq and Afghanistan.

Employees who left IRD were asked to sign confidentiality agreements stipulating that they could be sued for making disparaging remarks about the organization, including to “funding agencies” or “officials of any government.”

A Washington Post article on Monday about IRD reported on the confidentiality agreements and on the nonprofit company’s having hired numerous USAID officials.

Lawyers who reviewed the confidentiality agreements at the request of The Post said they could violate whistleblower protections under the False Claims Act. IRD has said it is changing its policy to “conform to the latest developments in employment law.”

John F. Sopko, the special inspector general for Afghanistan reconstruction (SIGAR), said his office is examining the confidentiality agreements.

During the past decade, International Relief and Development received more in grants and cooperative agreements from USAID than any other nonprofit organizations — $1.9 billion. The humanitarian group worked in Iraq and Afghanistan and provided 38 employees with $3.4 million in bonuses between 2008 and 2012. Here are the bonuses given to IRD employees compared to other nonprofits operating in hazard zones between 2010 and 2012.

“The threat of retaliation for reporting problems to oversight agencies is all too real,” Sopko wrote in a letter to IRD founder Arthur B. Keys.

Sopko asked IRD to disclose how many employees have signed the agreements and to alert those who have that the documents are “null and void.”

USAID also said its contractors should not be using confidentiality agreements containing such language.

“USAID contractors and implementing partners have an obligation to report allegations of waste, fraud or abuse related to USAID projects,” the agency said in a statement. “No contractor or partner should use nondisclosure agreements to limit the federally protected rights of its employees to report waste, fraud or abuse.”

An IRD spokesman said the company is cooperating with Sopko’s request.

“We are in the process of complying,” said William A. Pierce, senior director of APCO Worldwide, which IRD has hired as its media representative. “We look forward to working with USAID and SIGAR on these issues.”

Sopko also wrote to the administrator of USAID, Rajiv Shah, requesting that the agency “forbids the recipients of federal funds from using confidentiality agreements that prohibit their employees from talking to U.S. government officials.”

USAID Acting Inspector General Michael G. Carroll said Tuesday that his office will examine the “revolving door” of employees between the agency, IRD and other contractors.

At least 19 former USAID officials, several of them high ranking, have been hired by IRD.

The agency said federal rules do not prohibit USAID employees from taking jobs with its contractors. “However, officials who leave the Agency are prohibited from representing a new employer back to the federal government on particular matters, like a contract on which the former employee worked,” the agency said.