Rabat last month banned director Ridley Scott's film on the grounds that it contained a scene "representing God", which is forbidden under Islam.
The state-run Morocco Cinema Centre said the film would now hit theatres in the North African country from Wednesday after "several changes" to the original version.
The filmmakers "accepted in an exceptional case, the removal of two audio passages that alluded to the personification of God," the centre said.
The centre, which had labelled the film "an attack on the religious sentiment of Moroccans", said it had now given the green light.
Mounia Layadi Benkirane, the film's distributor in Morocco said around five seconds of the movie was being silenced.
"It's a half-victory because we would have wished it was not censored at all," she told AFP.
She said Scott, the director, had tried to assure the Moroccan watchdog that he had made every effort not to offend any religion. "With reluctance, he accepted the parts being removed."
The blockbuster based on Moses's flight from Egypt has also drawn accusation from Cairo and the United Arab Emirates of "religious and historical mistakes".
It earned $24.1 million in its debut weekend last month in the United States, according to box office tracker Exhibitor Relations.
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Scriptwriter did a good job not to offend religions. IN fact he was even charitable to the Egyptian pagan religion by making all the prophecies made by the court astrologer come true ! According to the movie, the art of reading entrails works !