Monday's punishments came six days after Phelps was apprehended by police in his hometown of Baltimore and charged with driving under the influence of alcohol, excessive speed and crossing the center line while driving inside a tunnel.
On Sunday, Phelps said on Twitter that he would be taking a break from swimming and "take some time away to attend a program" for treatment of unspecified personal issues.
In announcing sanctions against the Olympic superstar, USA Swimming executive director Chuck Wielgus said Phelps' actions required "significant consequences."
"We endorse and are here to fully support his personal development actions."
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The discipline meted out, which includes forfeiture of Phelps' funding from the federation for six months, is based on USA Swimming rules that prohibit conduct "detrimental to the image or reputation" of USA Swimming or the sport.
Phelps will still be allowed to train with his club, but cannot compete in USA Swimming-sanctioned competitions through March 6, 2015.
According to the federation, Phelps has agreed that he will not represent the United States at the World Championships on August 2-9 in Kazan, Russia.