A division bench comprising Chief Justice SR Bannurmath and Justice Thothathil B Radhakrishnan also directed the CBI to complete the investigations in six months' time.
The court's direction came on a petition filed by Muthoot business group chairman MG George, seeking a CBI probe into his son Paul's murder in August last year.
The court directed the police to hand over all relevant documents regarding the case to CBI.
During the hearing, police had told the court that investigations were carried out meticulously based on "true facts", but the bench criticised the police probe on several occasions.
The state government had also informed the court that it was not "afraid" of a CBI probe, contending that a fair investigation has been conducted by the state police.
Pressing for the CBI probe, the Muthoot family had submitted in the court that police had not properly recorded their statements, and had 'omitted relevant parts from their statements.'
The bench also criticised IGP Vinson M Paul, who headed the special investigation team (SIT), for conducting a press meet with regard to the investigation in the case.
The Kerala government had formed an SIT to probe the murder of Paul Muthoot, a young businessman of the multi-crore Muthoot group with diverse business interests, including finance and hospitality sectors.
The SIT had filed chargesheet in Ramankiri court in Alapuzha, listing 25 accused in the case. The magistrate had returned the charge sheet saying it was incomplete. However, the high court had stayed the order on an appeal by the state government.
Paul's father had filed the petition expressing dissatisfaction at the police investigation, and seeking CBI probe.
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