The post was retweeted more than 100,000 times in the first five hours after being made and was favourited 105,000 times.
The tweet seems unusual for Malik who usually posts message promoting One Direction singles and self portraits for his fans.
Earlier this month Barbadian pop singer Rihanna tweeted the same hashtag before deleting eight minutes later.
A source told US entertainment news website TMZ, which first reported the story, that the tweet was made by accident and should never have been sent.
Pop star Rihanna tweeted in support of Palestine using the #FreePalestine tag before deleting it several minutes later.
The message was retweeted 4000 times before it was deleted, Rhianna later tweeted that she hoped for a peaceful end to the conflict.
One of the NBA's most well-known basketballers - Dwight Howard of the Houston Rockets - apologisedrecently as well after using the hashtag in a tweet.
