The 12-time winner, who defeated Japanese star Kento Momota in last year's final, was initially scheduled to take part at the tournament and face Srikanth Kidambi of India in the first round after recovering from his nose cancer.
Although he was deemed fit, Lee opted to heed his doctor's advice to skip the tournament.
"Following his routine check-up in Taiwan, we are pleased to inform that Datuk Lee Chong Wei has been given a clean bill of health and his recovery process is progresing well," read a statement released by the national badminton body.
"However, in order not to put his body under undue stress, Chong Wei has been advised to withdraw from the upcoming Celcom Axiata Malaysia Open 2019.
"BAM's priorities remain focused solely on Chong Wei's health and will continue to offer the 37-year-old unwavering support.
"We also urge everyone to give him the space and time required for his recovery."
OFFICIAL: Statement on Datuk Lee Chong Wei’s Malaysia Open 2019 participation#BadmintonMalaysia#KebanggaanKita pic.twitter.com/V6zSuJX9lh
— BAM (@BA_Malaysia) March 19, 2019
The BAM did not provide a potential return date for the national badminton star, who is currently ranked outside qualification spots for the 2020 Summer Olympics.
The 2019 Malaysian Open is set to take place at the Axiata Arena in Kuala Lumpur from April 2nd to 7th.