The 27-year-old Brandt is the first rider to fail a dope test on this year's Tour.
"I don't understand. I have never heard about this product," Brandt told reporters. "I long to have the results of the B sample.
"Maybe tests should be made on the vitamins I took in recent days, but I never took methadone," he added.
Methadone is a potent synthetic narcotic drug, less addictive than morphine or heroin, which is used as a substitute for these drugs in treatment programmes for addicts.
It is also used for chronic pain management.
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Lotto-Domo manager Patrick Sercu said Brandt had been suspended after a first test on his sample proved positive last Monday following the second stage between Charleroi and Namur.
"Let's hope the second test will shed more light on the case," Sercu added. "But the cyclist could be fired if the second test also proves positive."
FOLLOWING INSTRUCTIONS
Team director Claudy Criquielion said he had decided to suspend Brandt in line with Tour de France instructions.
"We decided to take him out of the Tour to follow the organisers' instructions that riders seriously involved in a doping case should be excluded," he said.
"But we're very surprised and we have full confidence in Christophe as methadone is not a performance-enhancing drug."
Criquielion added that traces of methadone found in the rider's sample could have come from another product, such as an energy bar.
"I hope to be able to tell you in three days' time that Brandt is innocent," he said.
Britain's David Millar, France's Cedric Vasseur and Italian Danilo De Luca were not accepted for the Tour after being charged in doping cases.
Spanish rider Gorka Gonzalez was declared unfit to start after blood tests before the prologue in Liege, Belgium, last week.
(Additional reporting by John Baete in Brussels)
