The Luxembourg rider was pulled out of the Tour by his RadioShack-Nissan team on Tuesday even though xipamide does not trigger a provisional suspension according to the World Anti-Doping Agency (WADA) regulations.
"The result of the counter test was positive but for me nothing changes: I just know that I did nothing wrong," Schleck, who finished third overall in last year's Tour, said in a statement.
"I will therefore continue my search to find out how the substance could have entered my body.
"At the moment we are analysing minute by minute what exactly I have been doing, eating, drinking on the days before the control and on the 14th of July itself, who I met, what materials I came in contact with, what nutritional supplements I took."
His RadioShack-Nissan sports director Alain Gallopin said after the 18th stage that the result of the B sample analysis was not a surprise.
"It does not change anything for us as he had left the Tour already. It is up to him to prepare his defence," he told reporters.
Frank Schleck, whose brother Andy withdrew from the Tour before the start because of injury, said extra tests were underway.
I didn't take anything, I assume it must have been given to me by someone, or it could have happened through an accidental contamination, or it could be caused by something that is not yet known to me since we are still undertaking a number of analyses," he said.
"Since these extra analyses will take a few days, I will communicate again from the moment I have received the results of the extra tests."