Malik, who was arrested last month and shifted to Kot Balwal Jail in Jammu, will be facing questions related to funding of his organisation from the National Investigation Agency.
The court passed the order after the agency said there was evidence against Khaitan showing evasion of tax and needed to be quizzed on the black money stashed.
VVIP chopper case: HC seeks CBI, Christian Michel's reply on Tihar Jail plea against his phone calls
The trial court had in January allowed Michel to make international phone calls to his family, friends and lawyers and he was granted 15 minutes a week for making calls.
The authorities also told Special Judge Arvind Kumar that the accused had been granted all facilities according to the jail manual.
VVIP chopper case: Delhi court seeks Tihar's reply on ED's plea to question Christian Michel in jail
Special Judge Arvind Kumar also issued a production warrant for Tuesday against Michel after his lawyer alleged mental torture inside jail.
The Ministry of Home Affairs (MHA) released a statement following rumours over the health of the separatist leader, lodged in the Tihar jail since his arrest on July 25, 2017.
A day after the Pulwama attack on February 14, the Jammu and Kashmir government moved the apex court to shift a Lashkar-E-Taiba terrorist out of Jammu jail.
Tihar officials move application against order allowing Christian Michel to make calls for 15 minutes
Special CBI court on Monday gave permission to alleged Christian Michel for speaking to his family and lawyers.
VVIP Chopper case: Delhi High Court seeks reply from Tihar jail authorities on Christian Michel's plea
Michel, who was arrested in the UAE and extradited to India on December 4, was on Wednesday remanded to judicial custody till December 28.
Michel, who was arrested in the UAE and extradited to India on December 4, was remanded to 14 days judicial custody on Wednesday.
Lodged in Delhi's Tihar Jail, they are accused of actively running the Dukhtaran-e-Millat, banned under the Unlawful Activities (Prevention) Act, 1967.
Life almost shut its doors on the young woman after the police told her she and her mother were named in an FIR in an alleged case of dowry death.
Apart from household amenities, including mattresses, in their cell, the Chandras also enjoyed a separate office room having a computer with internet, a printer as well as eatables.
"Is there a parallel system running in jails? Do they have special rights in jails," asked the SC bench.
Singh was handed death penalty, the first capital punishment in the riot cases, whereas Sherawat sentenced to life imprisonment.