A bench of justices P Sathasivam and B S Chauhan rejected the plea of the Gujarat government that no CBI probe can be ordered as the state police has already filed a charge sheet in the case.
The apex court gave the direction on an appeal filed by Narmada Bai, mother of Tulsiram Prajapati, alleging that he was killed in a fake enounter by the Gujarat police as he was a key eyewitness in the Nov 2005 killing of Sohrabuddin Sheikh and his wife Kausar Bi.
The apex court said the petitioner had made out a strong case for transfer of investigation to the CBI as there was strong suspicion about the involvement of police personnel from three states -- Andhra Pradesh, Rajasthan and Gujarat.
The bench, however, clarified that whatever observation made in this judgement shall not have any influence on the trial judge dealing with the case.
It also criticised the tardy investigations conducted by the Gujarat police in the killings, in which, besides politicians, top police officials are also involved.
The bench regretted that the State police took more than three-and-a-half years to file the charge sheet after the killings.
The Gujarat government had during the arguments strongly opposed a CBI probe on the ground that Prajapati's killing was a separate encounter and in no way connected to the encounter of Sohrabuddin Sheikh.
The bench had on Mar 15 reserved its judgement after hearing at length for three days CBI, Gujarat government, Shah and petitioner Narmada Bai's counsel.
Gujarat and Shah, through senior counsel Ranjit Kumar and Ram Jethmalani, had opposed CBI's taking over the case on the ground that the Centre was trying to implicate the former Home Minister and Chief Minister Narendra Modi in the encounter deaths.
However, senior counsel K T S Tulsi for CBI and Huzefi Ahamadi for Narmada Bai had justified the transfer plea as according to them the investigation by the Gujarat police was "biased" and Prajapati's killing was a sequel to the encounter deaths of Sohrabuddin, an alleged extortionist, and his wife.
It was alleged by CBI and the petitioner that Sohrabuddin, Kauser Bi and another person, suspected to be Prajapati, were picked up during a joint operation by the police of Gujarat and Andhra Pradesh from a bus on their way from Hyderabad to Sangli in Maharashtra on Nov 22, 2005.
Sohrabuddin was gunned down in an encounter by the Gujarat police's Anti-Terrorist Squad. The policemen are also accused of killing Kauser Bi and Prajapati to destroy evidence.
The investigation in the case by CBI had stirred a political controversy after Shah was arrested and charged with killing Sohrabuddin and his wife.