The move means the 27-year-old will not have a repeat of the 2008 Summer Olympics, where he won eight gold medals and made history.
On the advice of his coach, Bob Bowman, Phelps decided to focus on the 200 and 400 individual medley and the 100 and 200 butterfly.
"It's so much smarter for me to do that. We're not trying to recreate what happened in Beijing. It just makes sense," he said.
Bowman said his main concern was Phelps being fresh for the 400 freestyle relay. While the U.S. has traditionally dominated that event, the Australians are favored for London. The relay was one of Phelps' closest calls in Beijing, with teammate Jason Lezak coming from behind on the anchor leg to beat a strong French squad.
The Associated Press contributed to this report.