Mo Farah's training partner Galen Rupp has taken the banned anabolic steroid testosterone since he was 16 under the supervision of the pair's coach Alberto Salazar, according to a television documentary to be screened on Wednesday night.

A wide-ranging investigation into the Nike Oregon project, the prestigious training camp in America where Farah has been based since 2011, alleged the existence of a culture where rules were stretched, bent – or broken.

The 29-year-old Rupp, who won 10,000m silver at the London 2012 Olympics behind Farah, was accused of being a regular user of the asthma drug prednisone, which is banned in competition. Meanwhile Salazar, a former marathon world record holder who is regarded as the best endurance coach in the business and has worked as a consultant for British Athletics since 2013, is said to have mentored Rupp to help him flout strict rules about using intravenous drips. Both men have denied any wrongdoing.

The most serious charges are made by Steve Magness, who was chosen by Salazar to be his No2 in 2011. Magness, a respected coach and author, told the BBC's Panorama that he was in Salazar's office when the reports showing the blood levels of every athlete in the Nike Oregon project were put on his desk.

“Under one of Galen’s it had ’currently on testosterone and prednisone medication’ and when I saw that I kind of jumped backwards,” explained Magness. “Testosterone is obviously banned and everyone knew that. It was all the way back in high school – and that was incredibly shocking. At that point I actually took a picture of it. I wanted to essentially to have evidence in case something happened.”

The programme showed Rupp's blood chart to David Howman, the chief executive of the world anti-doping agency, who said he was "disturbed and very disappointed".

Both Salazar and Rupp strenuously deny that the athlete has taken testosterone. In a statement Salazar said the legal supplement Testoboost had been “incorrectly recorded as ’testosterone’ medication”, and that “the allegations were based upon false assumptions and half-truths”.

Rupp added: “I have not taken any banned substances and Alberto has never suggested that I take a banned substance.”

Salazar is also alleged to have asked his son, Alex, to conduct laboratory tests to see how much testosterone cream would trigger a positive test. According to Magness, Salazar Jnr told him they were worried that someone could rub some cream on one of their athletes after a race. Magness said he believed that explanation to be "ludicrous" – and that they were instead trying to figure out how to cheat.

Magness, who left Salazar’s group after the London Olympics, said he had gone to the US anti-doping agency with his concerns but now feared the repercussions of speaking out. “It’s incredibly scary,” he said. “It would be much easier to just shut up, do my job. I’ve got a good job and reputation.”

The documentary reveals that six other people who were associated with the Oregon Project have spoken privately to Usada with concerns about alleged illicit practices and unethical behaviour. Usada declined to comment.

However none of the insiders said they had witnessed evidence that Farah was doping. And in a statement Farah said: “I have not taken any banned substances and Alberto has never suggested that I take a banned substance. From my experience, Alberto and the Oregon project have always followed Wada rules.”

However Farah is bound to face questions given his close relationship with the man whose training genius and cutting-edge scientific research helped him become the Olympic and world 5,000m and 10,000m champion. Last night Andy Parkinson, the former chief executive of UK Anti-Doping, warned: "Any athlete who's involved with this group, including Mo Farah, has a responsibility to ask themselves 'do I feel comfortable in this environment and am I going to be able to continue to compete clean in this environment?'."

Another unnamed runner who worked with Salazar for several years said that in 2007 he was feeling run down and went to see Dr Loren Myhre, the Nike lab's head physiologist before he died in 2012. That athlete claimed: "I did a blood test at Nike and my thyroid was low and testosterone was low. Dr Myhre suggested that I go and see an endocrinologist that Alberto and most of the athletes work with, to get testosterone and thyroid. He said 'this is what Alberto does. You'll feel better and you'll be able to train better', and so then I said: 'Well, isn't that cheating?' And he goes 'well no, Alberto does it'."

“I did mention something about being like, wouldn’t it test positive? He said, ’No, no, no. We’ll get you into the normal range’.”

Meanwhile Kara Goucher, the 10,000m world championship bronze medallist who trained at the Oregon Project until 2013, said that Salazar had coached Rupp to try to get a Therapeutic Use Exemption for an intravenous drip before the 2011 World Championships. Under Wada rules, such drips are prohibited and anyone caught manipulating the TUE process to get one would be liable for a ban.

“I had a conversation with Galen in 2011 and he told me how tired he was and how he was so excited to have the season be over,” added Goucher. ‚“And fast forward a month and he shattered the American record. That’s not how it works.”

The show's presenter Mark Daly also showed how apparently easy it is to avoid the biological passport, which is designed to detect athletes who take the blood-boosting drug EPO. Daly took micro-doses of the drug that were big enough to substantially improve his performance, but not too much to trigger a red flag in his biological passport.

The programme also quotes three witnesses who have made sworn statements to say that Allan Wells, who won 100m gold at the 1980 Moscow Olympics, was a regular steroid user. Wells denies the allegations.

(Guardian service)