"I categorically deny taking any banned substance. I have no explanation for the test result and therefore insist that the B sample be tested which is my right," Schleck said in a statement sent to Luxembourg media network RTL overnight.
"If this analysis confirms the initial result, I will argue that I have been the victim of poisoning," added Schleck, who was in 12th place in the overall standings.
Schleck, who finished third last year, was pulled out of the race by his RadioShack team immediately after the test result was announced.
He is not suspended because according to the World Anti-Doping Agency, Xipamide was "a "specified substance", which allowed for a greater reduction of a two-year sanction when an athlete tested positive for it.
The Tour de France was rocked on Tuesday when Schleck, who was third overall in last year's race, pulled out following the dope test result.
The older of the Schleck brothers - Andy won the Tour two years ago - was nine minutes and 45 seconds behind leader Bradley Wiggins.
"After being informed by the UCI about the presence of Xipamide in the urine sample of Frank Schleck on July 14, the team has decided to immediately withdraw Frank Schleck from the Tour de France," RadioShack-Nissan said in a statement.
RadioShack said Schleck had gone willingly to the police station and the team hotel had not been searched, although witnesses said uniformed and plain clothes police officers were on patrol in front of the building in Pau on Tuesday evening.
The doping test took place after the 13th stage on July 14 when traces of the specified drug Xipamide were found in Schleck's urine.
"On the subject of Xipamide the team can declare the following: It is not a product that is present in any of the medicine that the team uses and the reason for the presence of Xipamide in the urine sample of Mr Schleck is unclear to the team," RadioShack added.
According to World Anti-Doping Agency regulations: "A specified substance is a substance which allows, under defined conditions, for a greater reduction of a two-year sanction when an athlete tests positive for that particular substance."
RadioShack was the outfit of seven-times Tour champion Lance Armstrong who, along with team manager Johan Bruyneel, is involved in a doping investigation launched by the US Anti-Doping Agency. Both men deny any wrongdoing.
The news on the second rest day came as another blow for the Tour given the stature of Schleck, on the podium last year behind his brother who was himself handed the 2010 Tour title after Spaniard Alberto Contador was stripped of his yellow jersey on doping grounds.
Last year, Russian Alexandr Kolobnev left the Tour for a similar offence and was later cleared by his federation.
On the first Tour rest day last week, France's Remy Di Gregorio was arrested in his team hotel in Bourg en Bresse and put under investigation for possession of illegal medical devices. He was released on probation and denied any wrongdoing.