The singer, 21, shared the #FreePalestine hashtag with his 13million followers on Twitter, which quickly clocked up 130,000 retweets, reported Daily Mirror.
Moments after it was posted, Israeli fans began blasting the star, telling him to "kill himself" and threatening: "Let me kill you."
One wrote: "Zayn should say what he said I mean if we're such a terrorists like he said why wouldn't we kill him for saying that huh @zaynmalik (sic)."
Others are vowing he has now lost all his fans from Israel.
Zayn is not the first celebrity to be criticised for showing their support for Palestine. R&B star Rihanna also caused a stir posting a message of support to her 36.4 million followers a few weeks ago.