Federal investigators are looking into allegations that the Secret Service deviated from normal polygraphing methods in the wake of a Cartagena prostitution scandal — including claims that polygraphy experts inside the service were uncomfortable with the deviations.

Senior Secret Service managers are said to have ordered the unusual methods in a rush to take swift action and put the humiliating episode behind the storied law enforcement agency. But now the inspector general for the Service’s parent agency — the Department of Homeland Security — is probing whether such variations and rushing could have led to flawed conclusions and unfair punishments for some men implicated in the scandal, according to two individuals briefed on the probe.

The public disclosure last month that a dozen Secret Service agents and officers had gone out for a night of heavy drinking while on a presidential business trip to Colombia and returned to their hotel rooms with prostitutes raised questions about the agency’s culture, and whether Director Mark Sullivan would keep his job. As President Obama faced a stream of questions about his bodyguards rather than his international economic summit in Colombia, Sullivan assured the White House and Congress he would move rapidly to investigate and root out the problem agents.

Some individual agents whom the Secret Service identified as bringing women to their Cartagena hotel rooms the night of April 11 were subjected to multiple polygraphs, a departure from past practice, according to those briefed on the case.

The Secret Service also questioned some employees in significant detail about their sexual activities on the Colombian trip. In a typical misconduct investigation, however, the Secret Service uses a more general “national security” polygraph test that seeks to assess an employee’s truthfulness and whether their actions posed a potential risk to national security.

The sources said that some agents implicated in the Cartagena prostitution scandal were pressured to resign almost immediately after being shipped out of Colombia on April 13 — but prior to being given polygraph examinations. Some were separately put under significant duress during extended polygraph sessions, conditions that could lead to faulty or inconclusive results, the individuals said.

A spokesperson for acting Inspector General Charles K. Edwards declined to comment on the details of the probe, and whether it has interviewed any members of the Secret Service’s polygraphing unit.

Edwards did confirm in testimony before the Senate Wednesday, however, that he has opened a separate probe to interview the 12 employees implicated in the scandal. He indicated then that he plans to review how many polygraph tests and what types were conducted on agency personnel.

The Secret Service has moved to dismiss nine employees and has cleared three of serious misconduct.

The Post reported exclusively Wednesday that at least four of those employees are fighting the agency’s push to dismiss them, arguing they didn’t break any rules. Some argue they are single men allowed to make their own decisions on personal time. Others insist the agency supervisors tolerated such off-duty partying, in a culture that allowed what happened on the road to stay on the road.

The new inquiry will be trained on whether Sullivan’s internal investigation was rushed or whether the move to oust most of the men involved was proper, according to legal officials familiar with the case, who spoke on the condition of anonymity because of the nature of the inquiry.

Edwards said at Wednesday’s hearing his ongoing probe will expand to not just review how the agency investigated itself but also the broader culture of the agency.

His office plans to review notes from interviews with nearly 200 agency employees who were in Colombia and 25 employees at the hotels in Cartagena.

Edwards told lawmakers that he received his first briefing on the situation on April 13, the day that the 12 Secret Service employees were returned to the United States.

Staff writers David Nakamura and Ed O’Keefe contributed to this article.