The younger sister filed a complaint against Asaram's son, accusing him of repeated sexual assault between 2002 and 2005 when she was living in their Surat ashram.
The complaint against Sai was registered at Jehangirpura police station in Surat, while the one against his father Asaram was transferred to Chandkheda police station in Ahmedabad as the alleged incident took place there.
Asaram, 72, was arrested in August on charges of sexually assaulting a minor girl and has been in prison in Jodhpur since then.
The police have registered two complaints - one against Asaram and another against Sai - of rape, sexual assault, illegal confinement and other charges.
