Inaki Badiola was in charge of the San Sebastian-based side in 2008 and claims he uncovered payments for illegal supplements between 2001 and 2007
Badiola, who was in charge at the San Sebastian club between January and December of 2008, told the AS newspaper he uncovered payments for "doping products".
"In 2008, our board reported that in the previous six seasons, at least, the board had given [staff] money to buy medicines or products that, at that moment, were catalogued as doping products," the 48-year-old explained to AS.
Badiola claims he has two files with evidence of these transactions and an e-mail requesting payment for doping products, which he says was declined.
"They acquired substances which were not authorised. In fact, there is an e-mail which names some of the products they wanted to buy - and we did not authorise it. They are practices which should never have taken place."
Sociedad declined to comment on Monday, but LFP president Jose Luis Astiazaran (who was in charge of the Basque outfit between 2001 and 2005) released an official statement in which he denied any wrongdoing during his time at the club.
He stated: "During the period of my mandate as president of Real Sociedad, I never had any knowledge or suspicion that any illegal practices were being carried out with regard to the medical services, who always worked with the maximum ethics and professionalism."
Astiazaran also called Badiola's claims "totally false" and revealed he is considering legal action against the former Sociedad chief.
The allegations emerged as Spanish doctor Eufemiano Fuentes remains under the spotlight in the ongoing Operacion Puerto doping investigation. In court last week, Fuentes offered to reveal the identity of the 200 blood bags uncovered in raids on his premises in 2006 which, he said, included cyclists, boxers and footballers, but the judge declined to follow up.
The Basques narrowly missed out on winning La Liga in 2002-03, finishing second behind Real Madrid.