A statement issued by Schumacher's lawyer Michael Lehner said: "These tests were undertaken... with a number of possibilities of blood contamination, of mixing up samples and other circumstances which could have distorted the result."
The 27-year-old Schumacher is one of four riders to have failed drugs tests at this year's Tour de France.
According to the AFLD the German rider, who won both time trials, tested positive for the new generation of EPO blood booster Cera on July 3, two days before the start of the Tour, and on July 15, a rest day at Pau.
In October the German Cycling federation (BDR) said Schumacher, who was riding for the Gerolsteiner team at the Tour, was facing a two-year ban and a fine.
The cyclist himself has denied all knowledge of doping.
Lehner described the suspension as "arbitrary," and said his client had applied to the (BDR) for a professional rider's licence for the 2009 season.
"Stefan Schumacher is currently preparing for the next season and has already been training in Cyprus," the lawyer added.