The use of Agriflu and Fluad brands, both manufactured by Novartis, was suspended last week amid concerns first raised in Europe that some vials contained milky floating material.
However, the federal agency said testing by the manufacturer, Canadian government scientists and data from European researchers indicated the vaccines were safe.
The release said it was notifying healthcare providers that the vaccines should be allowed to come to room temperature before injection.
"The products should also be shaken and checked for any white floating material before they are injected," the agency said. "Such material is not uncommon in vaccines and does not pose a risk to health."
Agriflu is designed for use in people older than 6 months while Fluad is recommended for use in Canadians 65 years of age or older.
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