Salem Abdel Galil, a former religious endowments ministry official, had made the remarks on a television show he hosts, sparking a backlash in a country reeling from deadly church bombings by Islamist extremists.
The endowments ministry, which controls the country's mosques, said Abdel Galil would not be allowed to preach Friday prayer sermons unless he retracts his comments.
Naguib Gobrail, a lawyer and Coptic Christian activist, told AFP that a misdemeanor court scheduled a hearing for June 24 to look into his complaint against the cleric.
Abdel Galil had criticised Muslim clerics who say Christians and Jews are "believers," adding that the non- Muslims were "kuffar" -- an Arabic word for disbelievers denied heaven.
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"Yes they believed in Jesus and in Moses, and then they disbelieved in Mohammed," Abdel Galil said on the show aired by the private Mehwar broadcaster, which subsequently apologised.
His comments prompted the endowments ministry to "prevent him from ascending the pulpit unless he remedies the concerns and tension caused by his comments," it said in a statement on Wednesday.
"As some considered it hurtful to Christians, I apologise for the hurt feelings," he wrote in a Facebook post.
"The religious view of the corruption of non-Muslims' faith, in our opinion, is the same as them viewing our faith as corrupt," Abdel Galil said, adding that did not mean Christians should be attacked.
The controversy over his remarks comes as Muslim institutions in Egypt are pressured to take a tougher stance against Islamist extremists following the church bombings.
Suicide bombers from the Islamic State group had killed dozens of Coptic Christians in three church attacks in December and April.