He was referring to remarks by Bishop Bishoy, secretary of the Coptic Church's Holy Synod, who said that some verses of the Koran were inserted into the holy book after the death of the Prophet Mohammed.
Muslims believe the Koran was handed down verbatim by the Archangel Gabriel over a period of around 23 years of the prophet's life.
"Religious dialogue must be limited to common points... dialogue must be for the good of the country," Shenuda said.
"We should never discuss theological differences.
"The simple fact of bringing up the subject was inappropriate, and escalating the matter is inappropriate," he said.
During a recent talk, Bishoy said that certain verses of the Koran contradict the Christian faith and that he believed they were added later by one of Mohammed's early successors, Caliph Uthman Ibn Affan.
His remarks sparked outrage among both Christian and Muslim leaders, saying they could lead to sectarian tension.
On Saturday, Al-Azhar -- Sunni Islam's top religious body -- slammed Bishoy's comments.
"This kind of behaviour is irresponsible and threatens national unity at a time when it is vital to protect it," Al-Azhar's Grand Imam Ahmed al-Tayyeb said in a statement.
Egypt's constitution guarantees freedom of expression, but there is great sensitivity when it comes to religious matters. Simmering tensions occasionally flare up into violent incidents between Muslims and Christians in Egypt.
Three Egyptian Muslims are currently on trial for allegedly gunning down six Copts after they emerged from Christmas services in Nagaa Hammadi in southern Egypt.
Coptic Christians make up around six to 10 percent of the 80 million population and complain of systematic marginalisation and discrimination.
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