Hughes, a 20-year-old right-hander, rolled his ankle while performing conditioning exercises Friday at Legends Field in Tampa, Fla., where he was rehabilitating a strained left hamstring.
The Grade 3 diagnosis is considered the most severe possible strain, in which one or more ligaments are stretched and completely torn. The Yankees made Hughes' results public Wednesday, prior to the club's game against the Toronto Blue Jays at the Rogers Centre.
Yankees officials had hoped Hughes would return in mid-June. But now with the setback, the hurler won't even throw off a mound until somewhere from late June to early July.
The Yankees' first-round selection in the June 2004 First-Year Player Draft, Hughes made two starts for the Yankees this season, making his Major League debut on April 26 and suffering a loss against Toronto at Yankee Stadium.
Hughes' second start was far more impressive, as Hughes carried a no-hitter through 6 1/3 innings in a May 1 start against the Texas Rangers before feeling a grabbing sensation in the back of his left leg, which was later diagnosed as a Grade 1 strain of his left hamstring.
Hughes was 1-1 with a 3.38 ERA in two Major League starts this season, striking out 11 and walking four in 10 2/3 innings. He also made three starts at Triple-A Scranton/Wilkes-Barre, going 2-1 with a 3.94 ERA.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.