The capsules, which are largely used for joint health, have been recalled by US distribution firm NBTY which said it discovered the "issue" during routine testing of the product.
The recall marks yet another blow to the US supplement market, which is trying to boost its consumer safety image after it has been delt a series of blows.
Last month the Texas Attorney General charged supplement manufacturer Mannatech for illegal marketing.
According to the Office of the Attorney General, exaggerated claims relating to the therapeutic benefits of Mannatech's dietary supplements and products were used to unlawfully mislead consumers with cancer, Down's syndrome, cystic fibrosis and other serious illnesses.
In January, the Federal Trade Commission (FTC) set the stage for unlawful marketing practices involving dietary supplements by fining four well-known weight-loss pill marketers for $25mn.
The settlements also required the marketers of Xenadrine EFX, One A Day Weight Smart, Cortaslim and TrimSpa change their ad claims.
It also comes at a time when the country launches Good Manufacturing Practises (GMPs) - legislation set to boost standards and allow for inspectors to check purity, safety and legality in manufacturing.
However, a spokesperson for the Council for Responsible Nutrition, said: "It appears to be a very isolated one off incident," but declined to comment further.
It is not thought the suspect shark cartilage capsules had gone on sale in UK shops, but may have been available through internet and mail order suppliers.
Chondroitin sulphate, one of the most popular supplements for joint health, is extracted from animal cartilage like shark cartilage.
The supplement is usually sold in combination with glucosamine and, according to the Nutrition Business Journal, US sales for these combined supplements were $810m (€132m) in 2005.
While a routine test detected the bacteria, testing on additional batches of shark cartilage did not show any evidence of contamination.
Dr Judith Hilton, Head of Microbiological Safety at the Food Standards Agency, said: "The presence of salmonella in a food supplement is unacceptable and potentially hazardous.
It's important that consumers of these capsules check that their personal supplies are not affected."
Salmonella is the second-most-common cause of food poisoning.
Symptoms can include nausea, vomiting, abdominal cramps and diarrhoea.
In some cases, food poisoning can cause very serious illness or even death.
It can cause serious and sometimes fatal infections in young children, frail or elderly people, and others with weakened immune systems.
However, no illnesses have been reported to date.
The affected shark cartilage capsules were sold under the following labels Puritan's Pride brand shark cartilage capsules, Nature's Bounty brand shark cartilage capsules, Rexall Sundown brand shark cartilage capsules, Vitamin World brand shark cartilage capsules, and Natural Wealth brand shark cartilage capsules.