Malik, 22, is to return home to Britain as the rest of the band goes on to play shows from the Philippines to South Africa, through Europe and the United States.
“Zayn has been signed off with stress and is flying back to the UK to recuperate,” a spokesman for One Direction said.
“The band wish him well and will continue with their performances” in the Philippines and Indonesia.
The announcement came after pictures of Malik, who is engaged to Little Mix popstar Perrie Edwards, were widely shared online showing him close to another woman.
One of the pictures showed him holding hands with the blonde, while in another the two posed with his arm around her stomach.
Malik spoke out against speculation about their relationship by declaring his love for his fiancee.
“I’m 22 years old… I love a girl named Perrie Edwards. And there’s a lot of jealous f—- in this world. I’m sorry for what it looks like x” Malik wrote in a Tweet to his 14.1 million followers.
One of the world’s biggest pop music acts, One Direction will continue their world tour, which has dates through the summer before finishing with a string of sold-out concerts in Britain.
Due to perform in the Philippines this weekend, the band have had to pay a $4,500 bond each for Malik and Louis Tomlinson which would be forfeit if they used drugs in the southeast Asian country.
A video of Malik, 22 and Tomlinson, 23 apparently smoking marijuana in a car while on tour in Peru went viral last year and shocked the tattooed but baby-faced quintet’s hordes of female fans.
Malik, who is from Bradford in northern England, was picked to be in One Direction after each of the band’s five members auditioned separately to be on reality TV show X Factor in 2010.
His fellow band mates have not explicitly addressed the recent events on social media, though Liam Payne tweeted “What a day”.