The gold medallist was driving a Cadillac Escalade through the city when his vehicle collided with a Honda Accord.
The star and his two passengers emerged unscathed, but the female driver of the Honda was taken to a local hospital after reportedly complaining of "head and arm pain".
He was sent home after being quizzed by traffic cops, and admitted he had drunk one beer before getting behind the wheel, but police had no reason to demand a sobriety test.
However, he has received a citation for carrying a invalid driving license for his native Maryland, as he still carries a permit for Michigan, where he resided from 2004 until last year (09).
Phelps will not be fined for the citation, but is expected to appear in court to explain to a judge why he had not renewed his license for his new address, according to the New York Daily News.
Police insist the star has not received any special treatment because of his stellar swimming career - claiming they treated him like any other citizen.
Police spokesman Anthony Guglielmi tells the publication, "We had our very best eyes on the situation, and we're very well aware of his history and his notoriety. We wanted to make sure that everything was done completely by the book.
It's not the first time Phelps has got in trouble on the road - in 2004 he pleaded guilty to driving while impaired after he was pulled over by Maryland cops for running a stop sign. He was sentenced to 18 months' probation.