The 32-year-old world number 12 sat out the second half of 2017 after a knee operation following a first-round exit at Wimbledon in June.
The Swiss ace spent eight weeks on crutches following surgery to repair the damage.
He returned this year but has struggled and was forced to withdraw during a second round match in Marseille last month against world number 193 Ilya Ivashka of Belarus.
Wawrinka said he hoped skipping the hard court tournaments of Indian Wells and Miami would enable him to return refreshed for the clay court season.
“Unfortunately I need to announce that I won't be able to play in Indian Wells and Miami,” Wawrinka said in a statement.
“They are both amazing events but coming back from a big surgery is complicated and after having played a few tournaments I have discussed with my team that it is best for me to build on the progress and go back to practice.
“I've enjoyed being back on tour playing matches and this gives me even more motivation to go back on the practice court. My goal is to find my highest level again and in order to do that I will keep working hard every single day.”
Wawrinka, the 2015 French Open champion, said he was targeting the clay court season.
“I need to be patient and give my body the time it needs, but as of now my goal is to come back on clay,” he said.
“I love that part of the season and hope to be ready by then.”