Farah, who won gold medals in the 5000m and 10,000m races at the 2012 Olympics in London, has been training with his American mentor, Salazar, at the Nike Oregon Project since 2011.
His training partner and silver medallist in the 10,000m in London, US athlete Galen Rupp, faces claims he took the banned anabolic steroid, testosterone.
Farah is not accused of any wrongdoing and said: “I have not taken any banned substance.
“From my experience, Alberto and the Oregon Project have always followed WADA rules.”
The claims were made in a BBC documentary alleging widespread use of banned substances at Salazar’s training camps.
The allegations come from former athletes and staff of the Oregon Project, with Salazar being accused of using banned steroids and unethical practices. This includes allegations of supplying Rupp with testosterone since the age of 16.
None of Salazar’s athletes have ever failed a drug test, including Rupp, who is one of the most tested runners in America.
Salazar and Rupp both denied any wrongdoing, with the coach issuing a statement to the BBC, saying: “the allegations your sources are making are based on false assumptions and half-truths in an attempt to further their personal agendas.
“I believe in a clean sport and a methodical, dedicated approach to training and have never, nor ever will, endorse the use of banned substances with any of my athletes.”
Rupp, 29, said: “I am completely against the use of performance enhancing drugs.
“I have not taken any banned substance and Alberto has never suggested that I take a banned substance.”
Salazar won the New York marathon three years in a row in the ‘80s and competed at the Los Angeles Olympics in 1984.
He has since become one of the most successful coaches in the world and is known for pushing the boundaries including use of the latest scientific techniques.
