The second-ranked Djokovic said in a statement that his withdrawal is a "tough blow" because the Monte Carlo Masters is "his favorite tournament."
Djokovic is undefeated so far this year with a 24-0 record. The Australian Open winner didn't say how long he will be sidelined.
Djokovic has won 59 of 65 sets and four titles on three continents. He defeated top-ranked Rafael Nadal on Sunday in the final at Miami.
Djokovic was a 2009 finalist in Monte Carlo.