In a story Wednesday by ProPublica and BBC (http://bbc.in/1FudipG), former Salazar assistant Steve Magness accused Salazar of using doping practices for his athletes at the Nike Oregon Project.
The story quoted both Salazar and Rupp as denying any wrongdoing. Neither Salazar nor Rupp's agent, Ricky Simms, immediately responded to emails from The Associated Press.
Rupp won the silver medal in the 10,000 metres at the London Games, finishing behind another of Salazar's leading runners, Mo Farah of Britain. The story said no doping accusations have been made against Farah.
Salazar is considered America's most powerful running coach. He built his reputation as a coach after winning the New York Marathon three years in a row from 1980-82 and the Boston Marathon in 1982.
While none of the Nike Oregon Project athletes, which include Canadian Cam Levins, have failed a drug test, ProPublica and the BBC reported allegations that some of Salazar's methods included the use of banned steroids and unethical practices.
The story said U.S. Olympic distance runner Kara Goucher and at least six other former Salazar athletes and staff members have gone to the U.S. Anti-Doping Agency with their concerns. It said USADA has not confirmed or denied any investigations.
USADA CEO Travis Tygart did not return a telephone message left by The Associated Press.
The report states Rupp had been given testosterone in 2002, when he was 16. It interviewed Magness, who worked at the Oregon project in 2011. Magness said he saw a document showing Rupp's blood levels that showed he was on "testosterone medication."
"When I saw that, I kind of jumped backwards," Magness told the BBC. "Testosterone is obviously banned. ... Everybody knew that. When I looked a little further I saw it was all the way back in high school — and that was incredibly shocking."
Magness said when he questioned Salazar about the document, the coach said it had been a mistake. Magness did not respond to an email from AP.
Salazar declined to be interviewed for the program, but told the BBC in a statement the legal nutritional supplement Testoboost had been incorrectly recorded in the document as "testosterone medication."
He added that the "allegations your sources are making are based upon false assumptions and half-truths in an attempt to further their personal agendas."
Rupp denied ever using testosterone or testosterone medication.
"I am completely against the use of performance enhancing drugs," he told the BBC. "I have not taken any banned substances and Alberto has never suggested that I take a banned substance."
The program aired claims that testosterone was seen on several occasions by athletes and staff, including a massage therapist at an altitude training camp in Utah in 2008. The therapist was reportedly told by Salazar the testosterone was for his own use for treatment of a heart condition.
The BBC also alleged that Salazar tested testosterone cream on a human to find out how much it would take to trigger a positive drug test.
"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," he told the BBC in a statement.
The program also aired allegations about the alleged use of asthma and thyroid medication for enhancing performance.
Goucher told the BBC that Salazar had encouraged her to take the thyroid drug Cytomel to lose weight in 2011 after the birth of her son. She said the coach knew she did not have a prescription for Cytomel.
"No athlete within the Oregon Project uses a medication against the spirit of the sport we love," Salazar responded in a statement. "Any medication taken is done so on the advice and under the supervision of registered. medical professionals."
Goucher also said Salazar tried to get a therapeutic use exemption for an intravenous drip for Rupp ahead of races.
"They wanted the IV for whatever reason to make Galen feel better, and they were manipulating the system to get it," she said.
Salazar responded: "I have never coached an athlete to manipulate testing procedures or undermine the rules that govern our sport. and follow the process for TUEs."
Farah told the BBC that he has never used banned substances and was never encouraged to do so by Salazar.