Leading coach Alberto Salazar says he "will never permit doping" among his athletes.
He has written a 12,000-word open letter denying accusations he violated anti-doping rules.
They include claims he was involved in doping US record holder Galen Rupp - training partner of Britain's Mo Farah - in 2002.
The 56-year-old coach added: "I believe in a clean sport and hard work and so do my athletes."
Read Alberto Salazar's full statement here.
There is no suggestion double-Olympic champion Farah, who is part of Salazar's Nike Oregon Project (NOP) training operation in the United States, has broken any rules.
The BBC understands Salazar is being investigated by the US Anti-Doping Agency, to determine if anti-doping rules may have been violated.
At least six former Oregon Project members have been approached by investigators in the last month. Documents and medical records have been requested from some of those giving evidence. A key figure heading up the probe is Usada lead investigator, Bill Bock.
A BBC Panorama investigation in collaboration with US journalism organisation ProPublica claims that American distance runner Rupp, 29, was given the banned anabolic steroid testosterone in 2002, when he was 16 years old.
In his letter, Salazar denies that Rupp has ever taken a banned substance, and Rupp has also denied the claims.
No allegations were made against other NOP athletes in the investigation.
|Who is Alberto Salazar?|
|Born: Havana, Cuba (emigrated to US as a child)|
|Achievements: Three-time New York Marathon winner (1980, 1981, 1982), Boston Marathon winner (1982), US Outdoor Track & Field 10,000m champion (1981, 1983), US Cross Country Champion (1979), National Distance Runner's Hall of Fame inductee (2000), represented US at 1984 Olympics in LA|
Cuba-born American Salazar added in the statement, published on the NOP website, that his athletes had to "fully comply" with the World Anti-Doping Agency (Wada) code and International Association of Athletics Federations (IAAF) rules.
He continued: "I am saddened that these false allegations have been allowed to run with little care for the carnage in their wake.
"I am always extra cautious and take every step to ensure my athletes comply with the anti-doping rules."
Defending Rupp, who won Olympic 10,000m silver behind Farah in 2012, Salazar said: "Galen suffers from severe allergies and breathing issues. He is medically diagnosed as suffering from both asthma and Hashimotos disease, a thyroid disease.
"Galen is one of the hardest working, most honest and genuine athletes I have ever known. Galen has never taken a banned substance in violation of the Wada code."
Salazar, who claims the allegations were based on "nothing but innuendo, hearsay and rumour", goes on to highlight Rupp's medical history in detail as well as details of thyroid and asthma medicine use in the NOP.
He also provides figures to answer claims about the alleged abuse of therapeutic use exemptions, or TUEs, which permit athletes to use certain substances to treat some conditions.
"We currently have nine athletes in the Oregon Project. Since 2011, those athletes have had a grand total of four TUEs," said Salazar.
"From these numbers it is clear that the Oregon Project is not manipulating the TUE process in any way."
The lengthy document also addresses specific claims made by individuals in the investigation.
Following Salazar's open letter, Nike said in a statement: "Both Alberto and Galen have made their position clear and refute the allegations made against them, as shown in Alberto's open letter.
"Furthermore we have conducted our own internal review and have found no evidence to support the allegations of doping."
Salazar is an "unpaid consultant" for UK Athletics, which has promised a review of his role. It said: "The content of the statement will be referred to our Performance Oversight Group for consideration in their ongoing internal review."
A BBC spokesperson said: "We are confident in our programme and that it was right to air the allegations of the witnesses who appeared on it.
"We stand by our journalism and it is now for the relevant anti-doping authorities to investigate the allegations.
"The detailed allegations were put to Mr Salazar four weeks before the programme aired giving him the opportunity to address them in full.
"The BBC has also invited Alberto Salazar to be interviewed about the allegations, an offer which still stands. Almost two months after Mr Salazar was first made aware of the allegations, we welcome his more detailed response."