The now-retired civilian specializing in ballistics is suspected of having stolen and destroyed some 30,000 files containing highly sensitive information, public broadcaster Radio-Canada reported. The employee has not been formally charged.
A spokesman for Defense Minister Harjit Sajjan told AFP that a probe is underway but declined to comment further.
A court document seen by Radio-Canada says military police obtained a search warrant for a highly restricted area within a research facility run by Defence Research and Development Canada, located near a military base outside Quebec City.
This document says files were copied and then erased, such as photos of ballistic test results, videos of ballistic trials and munitions procurement records, Radio-Canada said.
The former employee under suspicion reportedly committed an act of insubordination before leaving his job with the army last year, Radio-Canada said.
He was reported by three former colleagues, it said.