The ruling means that Armstrong will have to decide whether to accept arbitration with the U.S. Anti-Doping Agency or face the possibility of a strict punishment, the Austin (Texas) American-Statesman reported.
U.S. District Judge Sam Sparks said Monday in a 30-page opinion that "the deficiency of USADA's charging document is of serious constitutional concern." However, he ruled that his court didn't have jurisdiction in determining whether Armstrong had used performance-enhancing drugs.
Sparks said federal courts shouldn't interfere with disciplinary procedures of an amateur sports organization "unless the organization shows wanton disregard for its rules, to the immediate and irreparable harm of a plaintiff, where the plaintiff has no other available remedy."
USADA sent Armstrong, a seven-time winner of the Tour de France, a letter in June accusing him and five people not involved in racing of a conspiracy to hide Armstrong's illegal use of drugs.
Armstrong contended the organization had no jurisdiction and that USADA had violated his right to due process.
USADA could issue a lifetime ban against Armstrong and strip him of his Tour de France titles.