Syeed Anees Shah will not be involved in any cases until further notice.
His comments last week drew attention from around the world.
He was overseeing a case in which a group of Christians were charged with lynching two men they suspected were involved in twin suicide bombings targeting a Sunday Mass at two churches in a Christian neighbourhood in Lahore on 15th March 2015.
He said that if they embraced Islam they would be free to go.
The men declined the offer.
According to the Express Tribune, Shah has been asked to report to the office of the Punjab Prosecutor General till further orders.
Welcoming his suspension, Wilson Chowdhry, Chairman of the British Pakistani Christian Association, said: "It is heartening to see that action has been taken by the Anti-Terrorism Court in suspending Mr Anees Shah, but quite frankly the whole debacle has only served to highlight ongoing prejudice in the Judicial system.
"Mr Shah's action implies that being Muslim places any citizen above the rule of law, a damning indictment of governance within the nation."