Armstrong was forced to withdraw Thursday from the Masters South Central Zone Championships this weekend after swimming's international federation raised objections to his participation.
Armstrong has been banned for life from sanctioned Olympic sport competition by the U.S. Anti-Doping Agency because of his performance-enhancing drug use during his professional cycling career. He had entered three distance events for the meet at the University of Texas and had been cleared by U.S. Masters Swimming officials to compete.
FINA stepped in with a letter to U.S. Masters Swimming officials, saying that because the organization falls under the FINA umbrella as a sanctioning body, it must recognize the World Anti-Doping Code and bar Armstrong from competition.
Armstrong spokesman Mark Higgins said Armstrong contacted U.S Masters Swimming weeks ago about racing. Armstrong, who is 41, was among the top qualifiers in the 40-44 age group in the 500, 1,000 and 1,650-yard freestyle events.
"As of (Wednesday) evening, we were told he was welcome," Higgins said in an email to The Associated Press. "That position changed and we were told he could not compete, so Lance will not be swimming."
U.S. Masters Swimming does not drug test. Before FINA stepped in, masters swimming executive director Rob Butcher had said Armstrong could compete because the organization was trying to promote its mission of encouraging adults to swim.
"His interest was around fitness and training. In light of FINA and the other political stuff, he will not be swimming," Butcher said Thursday.
FINA sent its letter after media reports surfaced Wednesday that Armstrong would compete.
"We're expecting them to apply the rules," FINA executive director Cornel Marculescu told the AP. A USADA spokeswoman did not respond to requests for comment.
Armstrong won the Tour de France from 1999-2005 and denied doping for years until USADA issued a massive report in 2012 detailing drug use by Armstrong and his U.S. Postal Service teams.
In January, Armstrong said during an interview with Oprah Winfrey that he used steroids, blood boosters and other banned performance-enhancing drugs and methods during his career. Armstrong also was removed from the board of the Livestrong cancer foundation he formed in 1997 after being diagnosed with testicular cancer that had spread to his lungs and brain.
Armstrong had been pursuing a post-cycling career in triathlons before he was banned by USADA.
AP Sports Writer Andrew Dampf contributed to this report from Rome.