Phelps, 29, the most decorated Olympian of all time, will also not represent the United States at the 2015 FINA World Swimming Championships in Russia next August, USA Swimming said in a statement.
"Membership in USA Swimming, and particularly at the National Team level, includes a clear obligation to adhere to our Code of Conduct," USA Swimming Executive Director Chuck Wielgus said in a statement.
"Should an infraction occur, it is our responsibility to take appropriate action based on the individual case. Michael's conduct was serious and required significant consequences."
Phelps was arrested last Tuesday after speeding and then crossing the double-lane lines inside a Baltimore tunnel, police said, adding he was clocked by radar traveling 135kmh 70kmh zone.
Phelps apologised for the incident and said on Sunday he was checking himself into rehab for six weeks in order to "better understand myself."
He can train with his member club, but is ineligible to participate in USA Swimming-sanctioned competitions through March 6, 2015.