Justice B Kemal Pasha passed the order on a petition by Aathikka, mother of 22-year old S Abdul Shukoor who was killed in Thaliparamba on February 20, 2012.
The petitioner alleged police were unable to collect evidence and probe further into the matter because of "stiff resistance and intimidatory tactics used" by the party of the accused.
"CBI cannot wash its hands off by saying that," the court said and directed the agency to investigate the case.
Jayarajan and Rajesh, arraigned as accused No. 32 and 33 in the case, have been charged with not trying to prevent the killing of Shukoor despite getting information about the conspiracy.
According to the police charge sheet, Shukoor was murdered because he was involved in an attack on Jayarajan and Rajesh while they were travelling in a vehicle.
Even the Director General of Prosecution had practically confessed before this court that the police machinery could not conduct a proper investigation because of the "intimidatory tactics and attitude of a particular political party of which A32 and A33 are leaders," the court said.
"If self-proclaimed kings of a locality are permitted to rule in the matter of investigation, criminal justice will become a casualty in their hands. The courts cannot remain mute spectators to such intimidatory tactics being played by such elements," Justice Pasha observed.
