According to police, Vikraman arrived at the Kannur first class magistrate's court on a two-wheeler around 11.30 a.m, forced his way into the court and surrendered.
The court later sent him to 14 days police custody.
Manoj and his friend Pramod were last week attacked by a group of men who threw a a bomb on their vehicle at Kathirur near here.
As the vehicle came to a stop, the armed assailants hacked Manoj to death, while Pramod survived the attack and is convalescing at the Kozhikode medical college hospital.
Police Monday took a statement from Pramod, who clearly identified the seven-member gang of assailants.
Ever since the murder, the name of Vikraman, who is allegedly close to the local Communist Party of India-Marxist (CPI-M) leaders was mentioned and a few days later, police named him as the prime accused.
Informed sources in police claimed that Vikraman was hiding in villages where the CPI-M enjoys very strong support but Bharatiya Janata Party and Rashtriya Swayamsewak Sangh (RSS) leaders alleged that Vikraman's surrender was stage managed by police and the CPI-M.
Meanwhile the state leadership of the CPI-M informed the party national leadership at the two- day politburo meeting which began in Delhi Thursday that the party has no role in this episode.
But the police probe team has already served notices to a few local CPI-M leaders to appear before them. On Wednesday, one party leader appeared before them but was let off after a few hours.
The Kerala government last week decided to hand over this case to the Central Bureau of Investigation (CBI) while the state BJP and RSS leaders have briefed union Home Minister Rajnath Singh about the case.
Manoj was one of the people accused of making an unsuccessful bid on the life of Kannur CPI-M district secretary P. Jayarajan in 1999.