Chief Metropolitan Magistrate Amit Bansal sent Tunda, 70, to police custody in connection with various bomb blasts in 1997 and for allegedly helping Pakistani nationals to infiltrate into India.
In a separate case related to 1994, Additional Sessions Judge Dharmesh Sharma sent him to judicial custody till Sep 21.
But the court order on Tunda's police custody will get precedence over the one on judicial custody.
Tunda was arrested in Uttarakhand's Banbasa area close to the Nepal border when he was trying to enter India Aug 16.
The Special Cell of Delhi Police sought Tunda's 10 days custody for interrogation over the 1997 bomb blasts in Delhi and adjoining areas in which 20 cases were registered.
Police said they had to establish the source of explosives which were provided to Pakistani nationals, arrested in 1998, in connection with 37 bomb blasts.
The police application for Tunda's custody said: "Contacts of the accused (Tunda), who helped in infiltration of Pakistani nationals arrested in the present case, are to be located/verified. Source of explosives is also to be established."
"The accused belongs to Pilkhuwa, Uttar Pradesh, from where the recovery of explosives was effected, and he is to be interrogated thoroughly in this regard," it said.
Advocate M.S. Khan, appearing for Tunda, opposed the police plea and told the court that "most of the accused arrested earlier in connection with these 20 cases had been acquitted as the recovery of explosives was not established".
He said there was no evidence to show that those arrested earlier had been in touch with Tunda.
The Delhi-born terrorist is suspected to be involved in over 40 bombings in the country. In Delhi, he is wanted in 21 terror cases related to 1994, 1996 and 1998.
An aide of fugitive don Dawood Ibrahim, the terrorist was also wanted for suspected involvement in the 1993 Mumbai serial blasts.