Moving to quell what one memorandum called the “collaboration” of the F.D.A.’s opponents, the surveillance operation identified 21 agency employees, Congressional officials, outside medical researchers and journalists thought to be working together to put out negative and “defamatory” information about the agency.

F.D.A. officials defended the surveillance operation, saying that the computer monitoring was limited to the five scientists suspected of leaking confidential information about the safety and design of medical devices.

While they acknowledged that the surveillance tracked the communications that the scientists had with Congressional officials, journalists and others, they said it was never intended to impede those communications, but only to determine whether information was being improperly shared.

The agency, using so-called spy software designed to help employers monitor workers, captured screen images from the government laptops of the five scientists as they were being used at work or at home. The software tracked their keystrokes, intercepted their personal e-mails, copied the documents on their personal thumb drives and even followed their messages line by line as they were being drafted, the documents show.