House Oversight and Government Reform Committee Chairman Jason Chaffetz (R-Utah) speaks on Capitol Hill. (Cliff Owen/Associated Press)

John Roth is the top watchdog at the Department of Homeland Security, a position shielded by law from outside pressure so he can conduct independent inquiries of the government’s sensitive internal workings.

But during a nearly completed investigation of the Secret Service, Roth’s office has taken the unorthodox step of allowing officials from the service to work alongside his agents as they tried to determine how unflattering information about a congressman was disclosed from the agency’s files, according to half a dozen people familiar with the inquiry.

Legal experts and former government investigators said the approach threatens the integrity of the investigation of who at the Secret Service uncovered and leaked material showing that Rep. Jason Chaffetz (R-Utah) — chairman of a House committee overseeing the agency — had once been rejected for a job as an agent. Chaffetz has been an outspoken critic of the Secret Service, which has been rocked recently by high-profile security breaches.

Secret Service staff members — inspectors from the agency’s internal affairs office who examine possible misconduct among employees — sat in on interviews with some of the more than 40 agents and officers questioned about the unauthorized disclosures, the people said. In some cases, the Secret Service inspectors contacted witnesses directly and questioned them along with investigators from the DHS Inspector General’s Office headed by Roth, who is responsible for examining alleged wrongdoing across the breadth of Homeland Security.

In one instance, Roth’s agents and Secret Service inspectors jointly questioned an agent about Carol D. Leonnig, a reporter for The Washington Post who has uncovered security missteps by the service, according to the agent’s attorney. Investigators asked about stories related to Chaffetz and other subjects and confronted the agent with his personal cellphone records, showing alleged calls and texts with Leonnig, the lawyer said.

The service’s involvement in investigating itself is problematic, experts say, because top officials at the agency had an incentive to embarrass Chaffetz. The participation of the service’s inspectors also could deter internal whistleblowers from coming forward with additional allegations of misconduct for fear of retribution by their bosses, the experts said.

“You just don’t do it. You don’t have the agency you’re investigating involved in the investigation,’’ said Eric Feldman, who held high-level posts in inspector general’s offices at four federal agencies in Democratic and Republican administrations and now advises companies on ethics. “That’s why you have an independent inspector general: to avoid the potential for conflict.’’

The agent’s cellphone records were obtained through an administrative subpoena issued by the DHS inspector general, people familiar with the probe said. Such subpoenas are a device that lawyers and former government officials say federal agencies increasingly use to force people and companies to turn over personal records and other documents without the prior approval of a judge.

Brady Toensing, the agent’s lawyer, condemned the use of the administrative subpoena and the Secret Service’s unusual involvement in the Chaffetz case. Toensing said the Secret Service inspector who questioned his client vowed to report the interview results “to his supervisors.’’ He said the questioning focused on the accessing of Chaffetz’s personnel file, which Leonnig had reported on April 2.

But Toensing said investigators also “went well beyond the Chaffetz matter” to explore in detail his client’s alleged contacts with Leonnig for several other Post stories in the weeks immediately after April 2. These included articles about a Florida postal carrier who landed a gyrocopter on the Capitol lawn and a top Secret Service official who the service said had resigned his leadership post but was still listed more than two months later in a senior position.

“You would think a poorly run agency . . . would commit itself to reform,’’ he said. “Instead, its management diagnosed the issue as a leak problem rather than misconduct and ineptitude. Consequently, it is hell-bent on finding and silencing whistleblowers.’’

Toensing agreed to be interviewed on the condition that his client remain anonymous.

Roth, a former senior Justice Department official who became DHS inspector general last year, declined to comment on the Chaffetz matter. But Roth emphasized the importance of the independence legally afforded all inspectors general, who investigate waste, fraud and abuse at federal agencies.

“The most important characteristic for an effective inspector general is his or her independence,’’ Roth said. “My independence is what allows Secretary [Jeh] Johnson and Congress to know that my office’s reports and recommendations are objective, truthful and made with integrity.’’

Erica Paulson, a spokeswoman for Roth, said that “generally speaking, it is not unusual” for the inspector general to receive help from internal affairs units within DHS.

“Our office has about 200 investigators with responsibility for investigating criminal and other serious misconduct in a department with more than 240,000 employees,’’ Paulson said. “In certain circumstances where we believe our independence will not be affected, we may use the components’ internal affairs agents as a force multiplier, relying on their help with investigative steps such as interviewing employees and gathering documents.”

People familiar with the Chaffetz case said the Secret Service is assisting with the inquiry. The report will be written by Roth’s office, they said.

The decision to involve the Secret Service was made without input from senior officials at the service or DHS headquarters, according to people familiar with the origins of the investigation.

In a statement, Secret Service spokesman Brian Leary said, “The U.S. Secret Service fully cooperated in the Department of Homeland Security Office of the Inspector General (DHS-OIG) investigation and provided support and assistance when requested by DHS-OIG.” He said that his agency could not provide any other information and that it is awaiting the final report.

Chaffetz said in an interview that he “has the greatest confidence” in Roth but that the Secret Service’s involvement in the inquiry “is a legitimate question that deserves an answer, an explanation.’’ He called the dissemination of his personnel file “a bit scary” and said that he hopes “appropriate action is taken.’’

Most of the Secret Service employees interviewed by investigators have been reprimanded, given one- or two-day suspensions or told they will face such disciplinary measures for accessing Chaffetz’s personnel file without a legitimate work reason, people familiar with the inquiry said. Some were accused of looking at information about the congressman, while others faced allegations that they passed along information to colleagues, the people said. It’s unclear whether other employees who were questioned will be disciplined.

The Post has reported that information about Chaffetz’s rejection for an agency job was circulated at Secret Service headquarters and in field offices within days of a contentious hearing in March at which he grilled Secret Service Director Joseph P. Clancy about the agency’s missteps. One official told The Post that the material included a parody poster that pictured Chaffetz leading a hearing on the Secret Service from his congressional dais, with the headline, “Got BQA from the Service in 2003.” Within the Secret Service, “BQA” is an acronym meaning that a “better qualified applicant” was available.

The disclosures about Chaffetz, which prompted apologies from Clancy and Johnson, were the latest embarrassment for an agency once considered the gold standard in law enforcement. Its repeated failures — which include allowing a White House fence-jumper to race deep into the executive mansion — forced the resignation last year of Secret Service Director Julia Pierson.

The White House and Homeland Security vowed reform. Clancy, a 27-year Secret Service veteran who once headed President Obama’s protective detail, has removed seven of the agency’s nine top managers.

A key reform Clancy has vowed to implement is greater encouragement of whistleblowers. He told Congress in November that he took the job partly because he was so disturbed that employees felt unsafe sharing their concerns with supervisors.

The law establishing federal inspectors general, passed in 1978, talks at length about the importance of protecting employees who report misconduct and requires IGs to designate a “whistleblower protection ombudsman.’’ The legislation does not address whether inspectors general can coordinate their investigations with the agencies they watch over, and the congressionally mandated body that represents IGs says such coordination is allowed.

But the body, the Council of the Inspectors General on Integrity and Efficiency, said in a paper last year that coordination generally involves IGs consulting with technical experts in an agency to make reports more accurate. The paper also warned against “the potential for conflicts of interest that exist when an audit or investigative function is placed under the authority of the official whose particular programs are being scrutinized.”

Former inspectors general and lawyers familiar with IG procedures said the Secret Service’s direct involvement in the Chaffetz case is unusual. “It’s a flashing red light that the inspector general’s independence has been compromised,’’ said Steven Aftergood, who directs the project on government secrecy at the Federation of American Scientists. “If they really are working collaboratively, that means any independent source the inspector general develops could be immediately exposed to the Secret Service.”

Roth has been outspoken about not being influenced by the massive department he oversees. He e-mailed all Secret Service personnel in October, saying he was starting an “independent review” of security breaches and encouraging employees to report wrongdoing. And he told the Senate Homeland Security and Governmental Affairs Committee in February that his goal was “to speak truth to power.’’

In the Chaffetz matter, Roth excluded Secret Service personnel from some interviews with “people who would be chilled by their presence,’’ said one of the people familiar with the investigation. Roth limited his use of administrative subpoenas to get phone records showing contacts with Leonnig, the person said.

Administrative subpoenas have been used by numerous federal agencies for decades, supported by court decisions that date back a century, legal experts said. Virtually all federal inspectors general have the power to issue them.

Christopher Slobogin, a Vanderbilt University law professor who has studied administrative subpoenas, said their use in the Chaffetz case was “on the outer edge of what could be considered relevant.’’

“It sounds like the investigators massacred the definition of relevance” by asking any questions that went beyond the Chaffetz matter, he said.

Mark S. Zaid, a Washington lawyer who has represented federal employees suspected of leaking information to the media, said Roth’s use of an administrative subpoena was appropriate “if there was a reasonable basis” to suspect anyone of leaking the Chaffetz material.