The move was expected as the International Cycling Union (UCI) had cleared Pereiro of a doping offence on Monday after he tested positive for salbutamol.
An AFLD source said the agency had received evidence from Pereiro showing his use of the drug was purely therapeutic.
Traces of the product were found in the Spaniard's urine during the 2006 Tour but the UCI said the test results could not be considered as a positive anti-doping control.
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The UCI said the Spaniard had shown "serious negligence" when he delayed providing evidence of a medical exemption to the AFLD requested in September last year.
French daily Le Monde reported earlier this month that Pereiro had twice tested positive for salbutamol during the Tour. Pereiro told Spanish media he had had an official medical exemption since March 2005.
The UCI said it had asked the AFLD to refrain from publicly implying a rider was guilty of a doping offence when he had committed an administrative fault only.
"The whole thing was pathetic," Pereiro told the Spanish television station Antena 3. "I want them to apologise for the mistake and try to rectify the damage they have done.
"It makes me even more determined to be declared the winner of the Tour if it is taken away from (Floyd) Landis."
Tour winner Landis tested positive for the banned male sex hormone testosterone during last year's race.
He faces a two-year ban from the sport and may be stripped of his title if his appeal before a U.S. panel of judges fails this year.
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