The nun, who has not been publicly identified, said she went to the police last year after complaining repeatedly to church authorities.
Eventually, a group of fellow nuns launched unprecedented public protests to demand Mulakkal's arrest.
Mulakkal has angrily denied the accusations, calling them "baseless and concocted".
In February, Pope Francis for the first time publicly acknowledged the sexual abuse of nuns by priests and bishops.
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies