The department says it has received reports of children getting sick after drinking the scented liquids used in the diffusers.
It says some of the formulations contain products that can pose serious health risks if swallowed by a child.
Reed diffusers are home fragrance devices; thin wooden sticks are inserted into a bottle containing scented oils and the reeds diffuse the fragrance into the surrounding air.
Health Canada says the decorative items can draw a child's attention and parents should make a point of telling children they pose a health risk.
It suggests that if a child does drink the fluid from a reed diffuser, parents should check with the nearest poison control centre or call 911.
The contact numbers for poison control centres are generally printed on the first page of telephone directories in the section entitled Emergency Numbers.