Packages of the pills made by Myland Pharmaceuticals should have three rows of active pills that are white and one row of placebo pills that are green.
Health Canada says missing one or more active pills could reduce the contraceptive's effectiveness and result in an unplanned pregnancy.
Those using the pill can return unopened packages to their pharmacists and are being asked to report any adverse reactions potentially related to recalled pills to Health Canada.
The company's other birth control product — Freya-21 — is not affected.
The recalled Freya-28 pills bear the lot numbers 3739F001B and 3739F002B.
The latest recall comes after a major birth control recall involving the drug Alysena 28 earlier this year.
One lot of the product contained too little active drug and too much placebo, leaving women who took it vulnerable to becoming pregnant.
The lot sold by a company called Apotex contained about 50,000 faulty packets and was distributed across Canada.
Women using birth control pills take the drugs for 21 days each menstrual cycle. Because of the risk that they might not remember to resume taking their pills at the right time, many oral contraceptives are packaged with a pill for each of the 28 days in a cycle — 21 are drug and seven are placebos.
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