On Sunday, the British News of the World tabloid published a photograph of Phelps inhaling from a marijuana pipe.
"USA Swimming has reprimanded Michael Phelps under its Code of Conduct by withdrawing financial support and the eligibility to compete for a period of three months effective today, Feb. 5, 2009," the U.S. Swimming Federation said on its official website.
Marijuana is not included in the list of prohibited doping substances complied by the World Anti-Doping Agency and may be used by athletes between competitions.
"This is not a situation where any anti-doping rule was violated, but we decided to send a strong message to Michael because he disappointed so many people, particularly the hundreds of thousands of USA Swimming member kids who look up to him as a role model and a hero," the U.S. federation said.
In marijuana-related scandal in Japan last year, three Russian sumo wrestlers were expelled from the 2000-year-old Japanese sport and banned for life after they tested positive for the drug.