A Winnipeg commander was not made aware the military was investigating an army reservist accused of ties to a global neo-Nazi terrorist group due to the type and nature of the probe, Canada's defence department said Friday.

The local chain of command was kept in the dark about the Canadian Forces National Counter-Intelligence Unit's investigation into Master Cpl. Patrik Mathews to protect his privacy and the integrity of the investigation, the Department of National Defence said in an email statement Friday.

The department is investigating whether Mathews is involved in a group with an international racist extremist agenda.

"While members of the individual's unit may be aware of an incident, unless the comments or behaviour are repetitive, or merit escalation, the Commander wouldn't necessarily be aware," the email reads.

Col. Gwen Bourque had not been alerted to the review of the eight-year member of the 38 Canadian Brigade Group based in Winnipeg when she spoke to media on Aug. 20, the department said. At the time, she said the military had no knowledge of his involvement with hate activities when he last worked with them in May.

Defence chief Gen. Jonathan Vance said in a Thursday press conference the reservist has been under investigation since April, when the military's counter-intelligence unit was first alerted to Mathews.

"Like with any investigative body, it's important that the integrity of that information be confirmed in order to protect the rights and privacy of the individual. This due diligence requires an appropriate amount of time depending upon the nature and severity of the allegations," the department said.

The DND would not say what prompted the military to look into the reservist's activity because it is an ongoing investigation.

The Mounties raided the reservist's rural Manitoba house in the town of Beausejour late Monday night and seized a number of firearms. RCMP spokesperson Rob Cyrenne had no updates by Friday on whether anyone was arrested, charges laid or weapons returned.

Watch: RCMP outside the Beausejour home

Video posted to social media shows the RCMP raiding a house in Beausejour on Monday evening. (video courtesy: Tyler Wenzoski) 1:40

In general, RCMP said in an email statement, Canadian Firearms Officers have the authority to issue or revoke a firearms licence, or to refuse an application altogether, based on their assessment of an individual's risk to themselves and others.

All current firearms licence holders are recorded in a database that is automatically checked every day to determine if individuals have been the subject of related incident reports and notifies officers when a person's licence is under review.

Police declined to comment on the case as the investigation continues.

Watch: How it felt going undercover with neo-Nazi terrorist group