A 132-page report recommended convening a tribunal to discuss possible legal and ethical violations by the World Anti-Doping Agency and to consider "appropriate sanctions to remedy the violations."
The French sports daily L'Equipe reported in August that six of Armstrong's urine samples from 1999, when he won the first of his record seven-straight Tour titles, came back positive for the endurance-boosting hormone EPO when they were retested in 2004.
Armstrong has repeatedly denied using banned substances.
The International Cycling Union appointed Dutch lawyer Emile Vrijman last October to investigate the handling of urine tests from the 1999 Tour by the French national anti-doping laboratory, known by its French acronym LNDD.
Vrijman said Wednesday his report "exonerates Lance Armstrong completely with respect to alleged use of doping in the 1999 Tour de France."
The report also said the UCI had not damaged Armstrong by releasing doping control forms to the French newspaper.
The report said WADA and the LNDD may have "behaved in ways that are completely inconsistent with the rules and regulations of international anti-doping control testing," and may also have been against the law.
Vrijman, who headed the Dutch anti-doping agency for 10 years and later defended athletes accused of doping, worked on the report with Adriaan van der Veen, a scientist with the Dutch Metrology Laboratory.
EPO, or erythropoietin, is a synthetic hormone that boosts the oxygen-carrying capacity of the blood.
Testing for EPO only began in 2001.