The agency is says it's due to a manufacturing defect that may render the device ineffective at delivering the medication in an emergency.
Allerject, which is used in the emergency treatment of anaphylaxis, works by reversing the rapid and dangerous decrease in blood pressure and relaxing the muscles in the airway during an allergic reaction.
A Health Canada statement says the defect "can pose serious health risks to patients" and that anaphylaxis may cause death.
The dosage for affected the pre-filled, single-use auto-injector is 0.15 milligrams and is intended for use in children weighing between 15 to 30 kilograms.
Health Canada did not immediately make it clear how much actual medication is involved.
Parents of children using this product are advised to check the lot numbers and return all affected products to their pharmacy for replacements.
The medication was distributed by Sanofi-aventis Canada Inc. since June 1 and the lot numbers in question are 2857508, 2857505 and DIN 02382059.
The company says the two batches amount to 3,039 of the auto-injectors.