"I believe in a clean sport and hard work and so do my athletes," said Salazar. "Apparently that is not interesting enough for some.
"I am very disappointed that the BBC and ProPublica and their 'reporters' who have allowed themselves to be used by individuals with agendas and have engaged in such inaccurate and unfounded journalism.
"Rather than present the facts, they opted for sensationalism and innuendo."
The United States Anti-Doping Agency (USADA) would not comment on whether Salazar's group was under investigation.
Rupp, the training partner of British double Olympic champion Mo Farah, denied ever using performance enhancing drugs. Farah has not been accused of any wrongdoing.
"I expressly told these reporters that these allegations were not true and their sources admit they have no evidence, yet they print 'suspicions' attacking me and sullying my reputation," said Rupp in an e-mailed statement.
"That is inexcusable, irresponsible journalism."
Rupp finished runner-up to Farah in the 10,000 metres at the London Olympics.
A World Anti-Doping Agency (WADA) spokesman said the agency had viewed the BBC programme and that any investigation would be up to USADA and the International Association of Athletics Federations (IAAF).
"We acknowledge that the programme also raises questions regarding the ability of athletes to dope by taking minimal amounts of performance enhancing substances without testing positive, otherwise known as 'micro-dosing,'" WADA said in a statement.
"It is an issue that we are exploring in great detail with experts."
(Editing by Peter Rutherford)
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