Maj.-Gen. Christopher Coates said bases were asked to take "precautions appropriate to their environments" to ensure the safety and security of personnel, equipment and buildings.
Across the country, different precautions were taken.
At Canadian Forces Base Edmonton, a spokesman said it was operating normally. But extra security precautions were put in place in Halifax and at 19 Wing Comox airbase on Vancouver Island in British Columbia.
In Halifax, gates to the waterfront navy base, the air base and other bases were locked as part of the heightened security effort.
Capt. Peter Ryan of Maritime Forces Atlantic said other measures can't be discussed in order to ensure the safety of military personnel, adding that the security measures weren't in response to any local incidents.
A Defence Department source said instructions were also sent by email on behalf of Rear Admiral John Newton to personnel advising them to avoid appearing in uniform in public places.
A spokesman for the Defence Department in Ottawa could not be reached for comment on whether a similar directive had been issued to military personnel across the country.
The source confirmed that the message from Newton asked staff "to restrict movement in uniform in public as much as possible."
At the 19 Wing Comox, 2nd Lt. Jennifer Halliwell said the base was implementing "additional force protection measures" to ensure the safety and security of personnel, although she couldn't offer specifics for security reasons.
A public affairs officer at Canadian Forces Base Esquimalt, just west of Victoria, said she wasn't aware of any additional measures in place at the facility.