Malik, who was brought up a Muslim, posted the hashtag #freePalestine to his 13 million followers today, and it has already been shared more than 140,000 times.
Among the abusive responses on the micro-blogging site, were messages telling him to "go kill yourself" while others called him "ignorant" and accused him of supporting terrorists.
Another told him: "The world hates you."
One pro-Israel fan said: 'You have fans in #Israel. It broke me that one of my idols wants me to die."
But other users praised him for the comment, provoking a heated debate among his fans.
Ahmad Ayyoub said: "thanks for being brave, thanks for being a human Zayn, free Palestine."
Another told him: "Don't let the hate messages you're getting deter you from speaking the truth! #FreePalestine."
Rihanna is among other celebrities to have spoken out in support of the social media campaign #freePalestine.
She tweeted the hashtag earlier this month before deleting it just minutes later, and instead posting a message asking people to pray "for peace and a swift end to the Israeli-Palestinian conflict".
One tweeter said: "Pathetic how people can support the killer state of Israel, whereas Zayn Malik Rihanna get threatened when they support #FreePalestine".