Embiid, a key figure in the Sixers' upset of the second-seeded Boston Celtics in the previous round, is suffering from right hip soreness and a right ankle sprain.
The news comes just hours ahead of Philadelphia's Game 2 against the Knicks at Madison Square Garden later Wednesday.
The Knicks dominated Game 1 of the best-of-seven series on Monday with an emphatic 137-98 win. Embiid finished with 14 points before being replaced midway through the third quarter.
Embiid underwent an emergency appendectomy in early April but returned for the final four games of the series against the Celtics, averaging 28 points as the Sixers recovered from a 3-1 deficit to win.