Karayil Rajan and Karayil Chandrasekharan surrendered before the chief judicial magistrate court here, which had yesterday issued non-bailable arrest warrants against them.
While Rajan is Kannur district secretary of CPI(M), Chandrasekaran is the Thiruvangad local committee secretary.
The court remanded them to 14-day judicial custody till July 5. The Kerala High Court had earlier rejected their anticipatory bail pleas.
The CBI, which is investigating the case, had earlier informed the court that the duo were the main conspirators.
The prosecution case was that a group of assailants had attacked Fazal, a former CPI(M) worker who switched over to NDF, and killed him in Kannur district.
The conspiracy was hatched to do away with Fazal as he had shifted his allegiance from CPI(M) to NDF and attracted more Marxist workers to NDF, it was stated.