Special CBI Judge Vinod Kumar said this after the agency informed the court that there was a "serious life threat" to Rajan from various underworld mafia groups and intelligence inputs have been received in this regard.
The Central Bureau of Investigation also said that MCOCA court in Mumbai may be requested to procure Rajan's attendance through video conferencing.
The agency said this in its reply filed on an application moved by the superintendent of Tihar Jail, where Rajan is currently lodged under judicial custody in an alleged fake passport case.
In his plea, the jail superintendent said a production warrant was issued by the MCOCA court at Arthur Road prison premises in Mumbai for his production before it today.
During the hearing on the plea, Rajan, who was produced through video conferencing, submitted that he was likely to be killed by his rivals if he is sent to Mumbai.
His counsel also said that sending Rajan to Mumbai may put his life under serious threat.
"I have considered all facts and circumstances and I am of the opinion that physical production of the accused before the MCOC Court is not feasible at this stage. However, the CBI is directed to request the State of Maharashtra to arrange production of the accused before the said court concerned through video conferencing," the court said in its order.
The court further said, "Copy of order be sent to jail superintendent, who has sought appropriate orders from this court on receiving production warrants from the MCOC special court, Mumbai."
It also said that the CBI should send a copy of its order to the special MCOC court in Mumbai immediately.
The case in which production warrant was issued was lodged against Rajan and others in 2011 under various sections of the Indian Penal Code, including 302 (murder), the Arms Act, the Mumbai Police Act and under the provisions of MCOCA.
In its order, the court noted that due to the threat perception to Rajan, he was being produced before it also through video conferencing.
The court had earlier ordered that remand proceedings in the alleged fake passport case, in which Rajan was arrested by the CBI, would be conducted through video conferencing from Tihar jail.
Deported after being on the run for 27 years, the gangster, whose real name is Rajendra Sadashiv Nikalje, 55, was sent to high-security Tihar prison in judicial custody on November 19 last year in connection with the case.
Rajan, once a close aide of fugitive terrorist and underworld don Dawood Ibrahim, has been brought to the country to face trial in over 70 cases of murder, extortion and drug smuggling in Delhi and Mumbai.
After his arrest in Bali (Indonesia) on October 25 last year, India had pressed for his early deportation.
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