Nevado was immediately suspended by his team Barloworld
Spanish rider Moises Duenas Nevado has tested positive for EPO, according to the head of the French anti-doping agency (AFLD), Pierre Bordry.
The Barloworld team cyclist was found to have used the banned blood booster during the Tour de France on 8 July.
"We have notified Moises Duenas Nevado that he had tested positive for EPO after the fourth stage," Bordry said.
Duenas Nevado has been detained by French police after an apparent raid at his team's base in Tarbes.
"I am stunned," said Barloworld team manager Claudio Corti in a statement.
"I want to go deeper in this story before (saying) something definitive and planning our next actions.
"It has emerged that some banned medicines that were absolutely not supplied or prescribed by the team doctor were found in Moises Duenas's room.
"The one thing I can certainly state is that the team is not involved in this at all, and will not sanction anything that damages our credibility and image.
"It's terribly disheartening but because the team is not involved, we hope that the whole truth can rapidly emerge so that we can take the necessary action."
The statement also said the rider had been immediately suspended by the team and withdrawn from the 11th stage of the Tour.
He is the second Spanish rider to test positive for the drug this year after veteran Liquigas rider Manuel Beltran was sent home following a positive test after the first stage.
Duenas Nevado was sitting in 19th place overall in this year's Tour after the first 10 stages.
Pat McQuaid, the president of the International Cycling Union (UCI), accused Spain of dragging its heels in the fight against doping.
"My first reaction is great anger," said McQuaid, reacting to the news about Duenas Nevado.
"It is interesting to see that it is the second Spanish rider (to failed a dope test on the Tour). Spain are slower to get the message."
The UCI barred Spaniard Alejandro Valverde from entering the World Championships in Stuttgart last year because of possible links to the Operation Puerto blood doping scandal that erupted in Spain in 2006.
The Spanish federation appealed to the Court of Arbitration for Sport (CAS), who ruled against the UCI, allowing Valverde to participate.
Spanish authorities also denied the World Anti-Doping Agency (Wada) and UCI access to blood bags seized during Operation Puerto.
In the lead up to the Tour the AFLD carried out approximately 60 random and targeted tests and, in the lead up to the start, blood samples were taken from all 180 riders.
Suspicion arose from these samples and Broadry said the Spaniard was targeted deliberately.
"We had reason to look at him more closely," he added.