The investigation should “determine the responsibilities and the failures that led to this regrettable release”, the statement said.
“The king was never informed in any way or at any time of the seriousness of the abject crimes of which the person concerned was convicted,” the palace added.
“It is clear that the sovereign would never have consented” to his release, given the “monstrous crimes” he committed, the statement concluded.
The pardon sparked outrage in the north African country, which has seen several high profile paedophile arrests in recent months.
Protesters slammed the pardon as “an international shame” with one demonstrator saying the state “defends the rape of Moroccan children”.
On June 20, police arrested a British suspected paedophile after local residents overheard screams from a six year old girl he allegedly abducted.
And in May, a Casablanca court jailed a 60 year old Frenchman for 12 years after convicting him of paedophilia.