The practice has led to some employees recently filing invasion-of-privacy lawsuits against their bosses, The Washington Post reported Friday.
Agencies not involved in gathering national security intelligence spent $5.6 billion in the 2011 fiscal year for hardware, software, personnel and other matters to protect classified information, the Information Security Oversight Office said.
Privacy advocates said the heightened monitoring increases the potential for abuse and the targeting of whistleblowers.
The groups said workers have had their personal e-mail accounts monitored when they were accessed using government computers. Monitoring software can overcollect information and supervisors have discretion about what they review.
Officials responded employees are more mobile and wired than ever, raising the possibility of accidental leaks of classified information.
The issue has caught the attention of Capitol Hill.
Congressional panels are looking into whether the Transportation Security Administration and the Federal Maritime Commission used intrusive software to monitor their employees.
Scientists with the Food and Drug Administration who were critical of some of the agency's decisions have sued over what they said was over-aggressive monitoring of their computers.