Justice B Kemal Pasha gave the direction while considering a plea filed by the parents of the slain Youth Congress worker, Shuhaib, seeking a CBI probe into their son's killing.
The judge directed the state police to hand over the probe to the Central Bureau of Investigation, besides the case diary and other materials to be handed over to the agency's Thiruvananthapuram unit.
Earlier, opposing the demand for the CBI probe, the state government argued that an impartial probe was being conducted into the incident.
All the accused were arrested and the investigation was progressing. Hence, there was no need for a CBI probe, the government said.
The petitioners contended that only 11 persons were arrested and there was no effective probe to identify those involved in the "conspiracy behind the murder".
The court held the view that the alleged conspiracy angle in the case should be investigated.
The CBI counsel informed the court that the agency was ready to take over the investigation in the case.
When the petition filed by the parents of Shuhaib, who was the Mattannur block secretary of the Youth Congress, came up for hearing on February 27, Justice Pasha had directed the state government and the CBI to file their replies by March 6.
They had also alleged that the probe was going on in a manner dictated by the ruling CPI(M) leaders in the state, who "control" the police machinery in the district.
The petitioners had also alleged that the police intentionally omitted to invoke the provisions of the Unlawful Activities Prevention (UAPA) Act in the case.
Since the prime accused, Akash, was close to those in the higher echelons of power, including the CPI(M)'s Kannur district secretary P Jayarajan, it was necessary to have a free-and-fair investigation in the case by the CBI, they had said.
The manner in which the brutal killing was planned and executed showed that there was a larger conspiracy which needed to be probed by an independent agency, without which it would be impossible to book the actual culprits, they had added.
Claiming that the ongoing police investigation was totally faulty and mala fide, the petitioners had sought an independent, free-and-fair probe into the case by a central agency.
No purpose of investigation would be served if the case was probed by the local police, which would be "partial, biased, motivated and prejudicial", they had said.
Shuhaib was hacked to death at a tea stall allegedly by CPI(M) workers on February 12.
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