The surveillance of these individuals was incredibly thorough, even overzealous. As described by the F.D.A. in a letter to Congress, the surveillance included screenshots taken every five seconds, all e-mails sent or received on the laptops, all data stored on or printed from the computers, all keystrokes performed, and data stored on personal thumb drives attached to the computers.

The agency says its governing laws require it to investigate and plug leaks of proprietary information, including trade secrets, and it contends that it has a right to monitor what its employees do on government-issued computers. That is true for legitimate purposes, such as detecting fraud, but in this case the agency itself may have crossed legal lines when it scooped up material submitted to or prepared for government agencies that investigate complaints from whistle-blowers, Congressional staff members and attorneys for the complaining scientists. The Whistleblower Protection Act and other statutes seek to protect the identities and allegations made by whistle-blowers to appropriate authorities.

In response to concerns about the snooping, the White House Office of Management and Budget last month distributed a memorandum urging all executive departments and agencies to ensure that their monitoring practices do not interfere with or chill employees from using appropriate channels to disclose wrongdoing.

Although the F.D.A. did not stop the whistle-blowers from communicating with outsiders, it did examine material being prepared for or submitted to the Office of Special Counsel, a separate body that accepts whistle-blower complaints from throughout the government, and to the inspector general of the Department of Health and Human Services. The memorandum said that monitoring designed to target (i.e. ferret out) such submissions would be “highly problematic” because it undermines the ability of employees to make confidential disclosures.

At this point it is difficult to say whether the whistle-blowers had strong substantive arguments about the safety issues or deserved to be overruled on the merits. We will know better how to judge this bitter dispute when separate investigations of the safety and retaliation issues are completed and when a separate lawsuit filed by the whistle-blowers is adjudicated in federal court.