Speaking to Iraqi media, Jafari underlined that methods employed by ISIL contradict the teachings of Islam, al-Wasat daily reported.
He said such acts of desecrating the Quran by ISIL only strengthen the resolve of Iraqi troops and volunteers to combat the terrorist group.
Iraqi forces launched an offensive on May 23 to retake the city, the first to fall to ISIL in Iraq in January 2014.
Iraqi Prime Minister Haider al-Abadi said on June 1 the offensive on Fallujah had been slowed down in order to protect civilians.
Humanitarian aid groups and residents said at the time that ISIL has trapped around 50,000 civilians, including 20,000 children, in Fallujah, threatening those who try to escape with death.
The Northern and Western parts of Iraq have been plagued by violence ever since ISIL terrorists began an offensive through Iraqi territory in June 2014.