Williams only returned to the top ranking in January after claiming a record 23rd grand slam singles title at the Australian Open.
"Sadly, I have to withdraw from the BNP Paribas Open in Indian Wells and the Miami Open," Williams said in a statement.
"I have not been able to train due to my knees and am disappointed I cannot be there. I will keep moving forward and continue to be positive. I look forward to being back as soon as I can."
