Walgreens has agreed to pay the Federal Trade Commission almost $6 million and change its advertising after the FTC claimed the company deceptively advertised “Wal-Born,” its store-brand cold and flu dietary supplement.

The FTC alleged that Walgreens improperly marketed Wal-Born by claiming it could prevent colds, fight germs, and boost the immune system. According to the complaint, Walgreens made such claims in advertisements in nationwide newspaper circulars, on its packaging, as well as on its Web site. The complaint also alleges that sales of the supplement from December 2004 through June 2009 exceeded $31.7 million.

The ads encouraged users to take the product “at the first sign of a cold symptom or in crowded places,” and touted the supplement as “Great tasting! Antioxidants! Amino acids! Electrolytes! 1000mg of Vitamin C! Seven herbal extracts! Take to boost your immune system before entering crowded germ filled environments, like airports, offices and schools.”

Under the terms of the settlement, Walgreens cannot claim that Wal-Born can boost the immune system or prevent or treat colds or the flu unless it has scientific proof.

The company will pay the FTC a total of $5.97 million.

In a separate settlement, the two principal officers of Improvita Health Products, Inc., the manufacturer of Wal-Born and other similar supplements, settled with the FTC for $565,000. The officers also agreed to ensure that their employees comply with the terms of the settlement.

Why it matters: The settlement is the latest action by the FTC taken against companies that advertise and market cold and flu remedies. In 2008, the FTC reached a settlement with the makers of Airborne totaling $23.3 million over claims that the company falsely advertised its herbal supplement. And last year, the FTC settled similar claims against Rite Aid and CVS over the stores’ in-house brands of supplements.