Desai, who has been charged with murder and conspiracy under sections 302 and 120(b), was produced yesterday before Additional Sessions Judge N P Dhote.
Setting aside a magistrate's order, the judge granted police his custody till June 24 to further investigate the role of HRS in the conspiracy and murderous attack on Shaikh.
The police had filed a revision petition before the court requesting eight days of police custody of Desai for investigating the murder case.
Earlier, police had sought Dhananjay's police custody to find out the flow of funds to the HRS, which was refused by Pune Cantonment court's judicial magistrate (first class) P D Zambare.
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On June 12, the magistrate court had remanded Desai and 20 others in 14 days judicial custody in connection with the murder till June 26.
Opposing the police remand, Desai's lawyers Chetan Bhutada and Atul Malviya said the HRS chief was being falsely implicated in the case and did not have any role in the alleged conspiracy.
The self-styled HRS head had already been in judicial custody in connection with another case registered in rural Pune for an inflammatory speech and circulation of provocative literature, when he was arrested by crime branch officials in the murder case.