A bench of Justice Dipak Misra and Justice Amitava Roy said that its order be communicated to the Bihar Home Secretary forthwith.
The court also said that no special privileges be extended to Shahabuddin in the course of his shifting.
The judgement was pronounced on a plea filed by Asha Ranjan, wife of Rajdeo Ranjan, the Siwan bureau chief of Hindi daily Hindustan who was shot dead in May last year.
Asha Ranjan has urged that Shahabuddin be shifted to Tihar to ensure a free and fair trial in the case.
Rajdeo Ranjan was shot dead in a busy market near Station Road in Siwan district by criminals on motorcycle as he was on his way home from office.
Ranjan worked for Hindustan -- a sister concern of Hindustan Times and one of Bihar's largest circulating newspapers.
Police have already arrested Upender Singh, an aide of Shahabuddin, in connection with Rajdeo Ranjan's killing. Singh is known as a sharpshooter of Shahabuddin.
Police in Siwan have said that Ranjan's killing was part of a pre-planned conspiracy.
The Central Bureau of Investigation (CBI) is probing the murder.
The apex court also asked the Patna High Court to decide in four months some of the matters relating to the cases against Shahabuddin pending before it.