The Food and Drug Administration’s chief operating officer said Wednesday that the agency’s new guidelines for monitoring employee e-mails will protect the rights of whistleblowers to communicate their concerns to Congress and others.

But agency officials said the guidelines would still allow them to conduct the kind of controversial surveillance that the FDA carried out in recent years against five government scientists. Officials said that monitoring was appropriate because the agency had reason to believe the scientists were releasing confidential company trade secrets.

“From where we were two or three years ago, it’s night and day,” Walter S. Harris, the FDA’s deputy commissioner for operations, told members of the House Oversight and Government Reform Committee at a hearing.

“We don’t consider whistleblowers outsiders,” Harris said. “We consider them part of our staff.”

His comments were met with skepticism by committee Republicans and some Democrats, who called the agency’s spying operation unacceptably invasive.

“The only thing that was missing was a camera looking both ways that would be reminiscent of George Orwell’s ‘1984,’ ” Chairman Darrell Issa (R-Calif.) said. He acknowledged that federal workers have no right to privacy on government computers or property. “But that is not to say that targeting is appropriate,” he said.

FDA officials have been under fire from Congress since the disclosure that they monitored the scientists’ computers as they wrote to congressional staff, their lawyers, journalists and offices that investigate government wrongdoing.

The agency says it suspected the scientists of disclosing confidential company information about medical devices they believed were unsafe. In a report released before the hearing, however, committee Republicans and Sen. Charles E. Grassley (R-Iowa) said the FDA may have overstepped federal laws meant to protect whistleblowers — and suggested the employees were targeted for retaliation.

By using software that searched for keywords and captured screen shots of their laptops at five-

second intervals, the FDA swept up material that’s protected by whistleblower laws.

“There was no effort to avoid snooping on legally protected communications,” said Grassley, who appeared as a witness. “They gave little or any thought to limiting what they were collecting.”

Some House Democrats, including Rep. Elijah E. Cummings (Md.), the party’s ranking member on the panel, defended the FDA, pointing to findings by the inspector general that oversees the agency.

In a review released before the hearing, the IG for the Department of Health and Human Services found the FDA’s concerns about leaks had been legitimate. That said, the review found the agency failed to “fully assess’’ the legality of whether the “potentially intrusive” scope of the operation would protect whistleblowers.

Angela Canterbury of the Project on Government Oversight questioned whether the new safeguards would protect whistleblowers’ communications. She said the FDA should not be in the surveillance or law enforcement business and suggested concerns about criminal wrongdoing go to the Justice Department.

Harris said the new monitoring policy makes sure that in collecting information about employees, any protected communications — for instance, e-mails to Congress — are flagged for review by agency lawyers, then discarded.

“We consider interactions with the Hill [and others] protected activities,” Harris said. “When we are going through the monitoring, they may walk upon that. And they’ll stop all processes.”

Harris also highlighted the usefulness of employee monitoring. He said such FDA efforts led to the conviction in 2012 of a chemist who used his access to the drug-approval process to make millions of dollars in an insider-trading scheme.

The case of the five scientists goes back to 2009, when FDA reviewers sent letters to Congress and the incoming Obama administration about alleged misconduct in the medical device office. They later took their complaints to the media, leading the FDA to ask the inspector general about a criminal inquiry into what the agency believed was leaked information. The IG turned them down. But the surveillance program moved ahead in 2010.

“The IT people collected information they thought met very narrow search terms,” Jeffrey Shuren, director of the agency’s Center for Devices and Radiological Health, told lawmakers. The terms included “colonography” and K followed by six numbers, the code for medical devices.

“Some of these appear to be the beginnings of a witch hunt,” Rep. Jackie Speier (D-Calif.) said.

The scientists had challenged approval of numerous imaging devices, maintaining that they did not work as advertised by their manufacturers, produced false positives and subjected patients to excessive radiation.

Asked by lawmakers if the scientists’ concerns turned out to be valid, Shuren said a committee of scientists that recently reviewed a CT scan approved for routine colon cancer screening unanimously found it safe for asymptomatic patients.

The whistleblowers were not called to testify Wednesday. Cummings said Issa was playing politics by not interviewing them as Democrats had wanted.

“Unfortunately, the majority has taken a traditionally bipartisan issue — something that all committee members should be investigating together — and turned it into another partisan spectacle for which our committee has become well-known,” he said.

Issa said the scientists’ allegations “have been confirmed independently” and added that he was “worried about [further] retaliation against them.”