Pettitte, 40, told the newspaper that he "did a little too much in Seattle" and that the ankle "hasn't healed up as much as [the doctors] thought it would."
He had been building arm strength by throwing on flat ground in the outfield before games, including on the club's recent trip to play the Mariners.
"He pushed himself too far, so we will back off," Yankees general manager Brian Cashman said.
Cashman added that Pettitte's situation is part of the "ebb and flow to rehab," and that the Yankees will "see him in September." Pettitte told the newspaper that he has been told to back off on his rehab temporarily to help reduce the swelling in the ankle.
The Yankees have expected Pettitte to return to their rotation in early September, and it is not believed that the latest issue with his ankle will affect the original timetable of six to eight weeks. Team doctors have been encouraged by periodic checkups on Pettitte's injury, including X-rays that have showed healing, and he has been walking without the help of crutches or a boot.
Pettitte suffered a fracture of his fibula when he was hit by a Casey Kotchman one-hop ground ball during a June 27 start against the Mariners at Yankee Stadium. He came out of retirement this spring after sitting out for the 2011 season, joining the big league club in May and going 3-3 with a 3.22 ERA in nine starts.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.