Raghavji, 79, was produced before Chief Judicial Magistrate Sanjay Pandey who sent him to judicial custody till July 22 and taken to Central Jail.
He told the court about his health problems after which the judge directed the jail authorities to ensure his proper medical care inside prison.
Raghavji's lawyer, Purshottam Panjwani, who moved his bail application in sessions judge Sushma Khosla's court, said it will be taken up for hearing tomorrow.
"Raghavji has been arrested from a flat in Koh-e-Fiza locality in old city area of Bhopal where he was hiding," Inspector General (IG) Bhopal Range Upendra Jain told PTI.
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The door of the flat was locked from outside and Raghavji was inside, police said. "When nobody responded, police broke open the door and found Raghvaji," the IG said.
After his arrest, he was taken to the Habibganj Police Station, where an FIR against him had been registered two days back.
Soon after the registration of an FIR, Raghavji, who celebrated his 79th birthday on Sunday, went missing from Vidisha.
The FIR was filed by his servant, Rajkumar Dangi who alleged that Raghavji abused him for the last three-and-a-half years on the promise of getting him a government job.
The victim prepared 22 CDs, which showed Raghavji in the alleged act, including one in Rewanchal Express Train.
Sources said that efforts were on to nab his two assistants, Sher Singh Chouhan and Suresh Chouhan, as the duo has also been accused in the sodomy case.
An embarrassed BJP government in the state found itself on the firing line of the Opposition. Assembly elections are due in the state later this year.