The 22-time Grand Slam champion, who has not competed since his Australian Open title defence ended in a second-round loss during which he aggravated a hip problem, said he had started rehab and physiotherapy as instructed by doctors.
"I am sad that I won't be able to compete at Indian Wells nor Miami. Very sad not to be there," read a message posted on Nadal's Twitter account. "I'll miss all my US fans but I hope to see them later this year during the summer swing."
The Spaniard is a three-time champion at Indian Wells having triumphed in 2007, 2009 and 2013. Nadal has reached the Miami final five times but has never won the title and has not competed there since 2017.
"We wish Rafa continued healing, and hope to see him back at the BNP Paribas Open next year," Indian Wells tournament director Tommy Haas said in a statement.
At the Australian Open, top seed Nadal tweaked his left hip while running for a backhand in the second set at Rod Laver Arena, and after inspection from a trainer when trailing 6-4 5-3, he went off-court for a medical time-out.
The 22-times Grand Slam champion returned grim-faced to play out the match but his movement was clearly affected, paving the way for American Mackenzie McDonald to end the Spaniard's bid for a third title at Melbourne Park.