The backup sample confirmed Frank Schleck had tested positive for a banned diuretic at the Tour de France.
The Luxembourg rider maintained Friday that he has not doped.
"The result of the counter test was positive but for me nothing changes," Schleck said in a statement. "I just know that I did nothing wrong!"
The RadioShack Nissan Trek leader was pulled from the Tour on Tuesday after the International Cycling Union said he had tested positive on July 14.
The first positive test on Schleck, who finished third in last year's Tour, jolted this year's race, and revived the doping allegations that have long tarnished the image of cycling.
After the first test, Schleck said if the backup sample eventually confirmed it, then a complaint would be filed "against an unspecified person for poisoning."
He made no mention of poisoning or a legal complaint in Friday's statement, but said he was determined to find out how the diuretic, Xipamide, had turned up in his system.
"Since I didn't take anything, I assume it must have been given to me by someone," Schleck said, suggesting that he could have consumed the banned substance "through an accidental contamination, or it could be caused by something that is not yet known to me."
The rider said he had witnessed the analysis of the backup sample at the WADA-accredited anti-doping laboratory in Chatenay-Malabry south of Paris. After seeing it test positive, Schleck vowed to "continue my search to find out how the substance could have entered my body."
The diuretic is classified as a specified substance and does not require a provisional suspension. The World Anti-Doping Agency defines "specified substances" like Xipamide as those that are "more susceptible to a credible, non-doping explanation."
Athletes who dope often take diuretics like Xipamide to mask other banned performance-enhancing drugs, or as a supplement for weight loss, according to the "Dictionary of Doping" by Jean-Pierre de Mondenard, a French expert.
Bans for such substances are often shorter, and athletes have a better chance of proving that they did not intend to consume it or enhance their performance.