It says contract tracing is underway and testing is being offered at the three institutions affected.
The five inmates—two in Drummondville, Que., one in Stony Mountain, Man., and two at the Edmonton Institution for Women—are medically isolated and being monitored.
None of the federal facilities is currently allowing visitors.
As case counts spike across the country, the correctional service says it continues to screen employees and equip correctional officers and inmates with medical masks, on top of heightened cleaning measures.
The federal justice and correctional systems have taken several steps to reduce the number of people in custody to lower the risk of transmission, including early release of low-risk offenders, extended parole and alternatives for those awaiting trial or sentencing.