Alberto Salazar strongly protested his innocence as he broke his silence on the drug allegations surrounding his Nike Oregon Project yesterday.

The Argentine published a 12,000-word letter refuting any suggestion that he had encouraged elite athletes to dope and said he believed in a “clean sport and hard work”.

Salazar, who is now under investigation by the US Anti-Doping Agency, has been accused by the BBC of giving Olympic medallists Mo Farah and Galen Rupp the banned anabolic steroid, testosterone.

“I will never permit doping,” Salazar said. “At no time do we use science in violation of the WADA Code. We strictly adhere to competition and anti-doping rules at all times.

“I have not and will not condone any athlete I train using a banned substance and would never encourage any athlete to use a banned substance. We have worked very, very hard to achieve our successes and are proud of our accomplishments.”

The comments were Salazar’s first in more than two weeks since the allegations were made, and many in the sport were disappointed by the amount of time it took him to respond.

Chris Estwanik, the six-times Bermuda Day Half-Marathon Derby winner, briefly worked with Salazar when he was a member of the Nike team in California in the early 2000s and remembers a man with an incredible reputation who “pushes the limits in every sense of the word”.

“When I was running for Nike our group was based in California and his group was based in Oregon, Ashley [Estwanik] and I were paid rabbits [pacesetters] for a few of his athletes,” Estwanik said.

“He was read his last rites once or twice after races because he had literally run himself to the point where he had a 108° fever, and pushed his body better than anybody in the world in his era as an athlete. I think he’s brought that same intensity as a coach.”

Salazar has also been accused of coaching Rupp and others to manipulate therapeutic use exemptions (TUEs), in which athletes can use otherwise banned medications or treatments for medical reasons.

The Cuban-born coach denied those charges and said Rupp, who was identified in the allegations, had been treated for asthma for several years. “Galen [Rupp] takes asthma medication so he can breathe normally — not so he can run better,” Salazar said.

Whatever happens Estwanik just wants the truth to come out, so that the sport he calls one of the “purest” there is does not suffer the same fate as cycling.

“It is disappointing that drugs are still so rampant, but people become obsessed with the sport, obsessed with the idea of beating a personal best or breaking a record and they lose sight of their morals,” Estwanik said.

“I’m sure most [athletes] say ‘I’ll never take drugs, I’m going to do it the clean way’, and they get out there and realise maybe they aren’t good enough with out it. The temptation is there and they overstep that mark, and go down that horrible path.”

The fallout from the endemic doping in cycling is still being felt, and no matter who wins the Tour de France this year there are sure to be questions marks hanging over any cyclist that performs above expectations.

Estwanik’s greatest fear is that the same should happen to his sport.

“I hope the truth comes out,” he said. “That’s all you want, and the punishments [if needed] are fair and the sport continues to clean up its act. If you don’t have a clean sport no one believes the times are pure and people will lose interest.”