The FDA used spy software designed to help employers monitor workers and capture screen images from the government laptops used when they working from home.

A detailed surveillance, of the five scientists in question, included monitoring of keystrokes, personal e-mails, documents on personal thumb drives and line by line messages which were captured by the agency.

A dispute lasting years between the scientists and their bosses at the F.D.A. fueled the intense scrutiny of the information.

The scientists’ claims that faulty review procedures at the agency had led to the approval of medical imaging devices for mammograms and colonoscopies that exposed patients to dangerous levels of radiation is at the center of this investigation.

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.