"It's been a massive misunderstanding and I hope those responsible for it apologize," the Spaniard told Radio Marca.
"It's true I took this product but it has been approved by the doctor and the UCI (International Cycling Union) and I am permitted to use it whenever I need to."
Pereiro said both the Tour organizers and UCI were aware that he had permission to take the product.
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"Since March 2005 I've been allowed to use it to combat allergies and when I have a cold. The permit has been renewed each season," the Caisse d'Epargne rider said.
"I'm very calm about the whole thing and know it will be sorted out when I send the paperwork tomorrow, but I'm upset that my reputation might have been stained by this report."
French anti-doping agency (AFLD) President Pierre Bordry told L'Equipe: "This rider tested positive twice. Once in Gap and another time in La Toussuire.
"Each time, he wrote on the test report that he had a TUE (Therapeutic Use Exemption). But I am asking him to provide us with the medical elements that justify him taking salbutamol."
Tour champion Floyd Landis also failed a dope test during the race, for the male sex hormone testosterone, and is likely to be stripped of his title and banned for two years if he fails to prove his innocence at an appeal hearing.
As runner-up to the American, Pereiro would expect to be awarded the victory if Landis is unsuccessful.
Mathieu Desplat, a spokesman for Tour organizers the Amaury Sport Organization, said: "We are waiting until January 25 when Pereiro's case will be reviewed by AFLD before taking any action."
Neither the Caisse d'Epargne team nor the UCI were immediately available to comment.
The director of Spain's government-run Sports Council Rafael Blanco told Spanish media: "From our point of view this isn't a positive test and Spanish authorities have not received any communication about any positive.
"The whole thing seems to have occurred because of a conflict in responsibilities between two institutions (in France).
"If there had been any doubt about the authorization to take such substances then they make the checks immediately and if there had been the slightest suspicion about Pereiro they would already have made that clear."
Last year's Tour de France was marred by doping problems. A day before the start, nine riders were kicked out of the race over a blood doping scandal that had erupted in Spain in May.
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