"Madrid, unfortunately I won’t be able to compete this year. I’m continuing my recovery in order to be back soon," Djokovic, who has struggled with a shoulder issue, wrote in a post on X.
He told Spanish broadcaster Movistar+ at a EuroLeague basketball game in the Spanish capital on Thursday that he was "struggling physically a little bit with an injury" but expressed hopes of playing in the tournament.
The 38-year-old Serb lost to Carlos Alcaraz in the Australian Open final in February and fell to Jack Draper in the Indian Wells fourth round last month, before pulling out of the Miami Open due to a right shoulder injury.
The 24-time Grand Slam champion then skipped last week's Monte Carlo Masters before arriving in Spain to begin preparations for the April 22-May 3 Madrid Open.
The draw for the tournament will be held on Monday.
Djokovic will be looking for a record 25th Grand Slam title when Roland Garros gets under way on May 24.