Malik's departure comes a day after he hit back on Twitter at rumours of trouble in his relationship with fiancee Perrie Edwards of the band Little Mix after he was photographed with another woman.
He tweeted: "I'm 22 years old ... I love a girl named Perrie Edwards."
This week, authorities in the Philippines said they were imposing a $5000 "weed bond" on Malik and fellow band member Louis Tomlinson, with the money to be forfeited if they were caught using or promoting illegal drugs.
"The condition is intended to protect the public interest should the band members commit any violation during their stay in the Philippines," bureau spokeswoman Elaine Tan said.
Malik and Tomlinson appeared in a video, which circulated online last year, in which they appeared to smoke cannabis and joke about drug use.