Chief Judicial Magistrate, Alipore Court, Rajesh Chakraborty accepted the remand prayer of Mumbai Police and directed it to produce him before a designated Mumbai court by September one.
The judge rejected the bail prayer of Khanna, who claimed he was innocent.
Indrani, wife of former Star India CEO Peter Mukherjea, was arrested by the Mumbai Police on Tuesday following leads by her driver, who was also taken into custody, in connection with the disappearance and murder of Sheena.
Khanna, a resident of upmarket Hastings Road area here, was arrested from his friend's flat at Alipore.
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He said Khanna had gone to meet Vidhie, his daughter from his marriage with Indrani, but had returned the next day after failing to meet her.
Appearing for the Mumbai Police, public prosecutor Sourin Ghosal opposed the bail plea and prayed for a seven-day transit remand.
Ghosal claimed before the court that Khanna was directly involved in the crime and had been named by the driver of Indrani, another accused in the intriguing case.