The joint team conducted raids at Asaram's ashrams at Rohini, Najafgarh, Jafarpur Kalan and on Ridge Road.
The sexual assault complaint against Asaram and Sai was filed at Jehangirpura police station in Surat.
According to police sources, the team from Surat landed in the national capital after tracing Sai's location to the city while intercepting his mobile phone locations.
Police, however, could not make any headway in finding out the whereabouts of Sai, who they said was frequently changing his location. There are apprehensions that he might have slipped into Haryana from Delhi.
Surat police had recently registered two complaints - one against Asaram, the other against Sai - of rape, sexual assault, illegal confinement and other charges as alleged by the two sisters.
The younger of the two sisters has filed the complaint against Sai, accusing him of repeated sexual assault between 2002 and 2005, when she was living at the Surat ashram.
Sai had filed for an anticipatory bail in a Surat court, which adjourned the hearing on the same yesterday after the prosecution sought time to submit a detailed reply on it.
Asaram, 72, was brought to Ahmedabad on Monday evening on a transit remand from a court in Jodhpur, where he was lodged in a jail since August in another sexual assault case.
A magisterial court in Gandhinagar yesterday remanded Asaram in four-days' police custody.
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