The CPI-M criticised the CBI for its action. The party's state secretary Kodiyeri Balakrishnan termed it as "nothing but a political conspiracy".
"This is being done at the behest of the BJP national leadership and meant to appease the BJP and the RSS in Kerala.
"Till yesterday, the CBI said Jayarajan is not an accused and today, they say he is. He was not even questioned, then how come the CBI arraigned as an accused?" Balakrishnan asked reporters.
A court near here on January 19 rejected the 63-year-old Jayarajan's anticipatory bail plea in the murder case.
Manoj, who was among a group of people accused of making an unsuccessful bid on Jayarajan's life in 1999, was on September 1, 2014, attacked by a seven-member gang in Kathirur near Kannur.
The assailants first hurled a bomb at the RSS activist's vehicle and later hacked him to death.
Jayarajan, a former legislator, was asked to appear before the Central Bureau of Investigation (CBI) earlier this month, but he moved an anticipatory bail plea in a court, which was rejected.
When he complained of uneasiness, Jayarajan was on Tuesday admitted to a hospital near here. Jayarajan is currently on bail in another murder case.
Though a similar anticipatory bail petition was rejected last year as well, Jayarajan was then questioned by the CBI in the state capital.
The probe agency has so far arrested 24 people in the case.
State Congress president V.M. Sudheeran, who is on his state-wide political yatra, on Thursday said he failed to understand why the CPI-M "is trying to run away?"
"Instead of facing the law, they are trying to run away and are challenging the legal system and also deceiving the people," said Sudheeran.