Additional Chief Judicial Magistrate S Gopalakrishnan issued the warrant for the second time on Tuesday as police had not informed the court that Nayanar had died when the court issued the warrant for the first time in the case in January 2007.
The case, relating to a collectorate blockade organised in 2002 by the Communist Party of India-Marxist, was considered by the court several times over the years.
All these years, the local police had failed to produce Nayanar's death certificate or furnish a report before the court in the matter as required by the legal process.
According to legal circles in Thiruvanthapuram, the filing of death report by the police is necessary to close the case against Nayanar.
A three-time chief minister, Nayanar died on May 19, 2004. A total of 19 CPI-M workers figured as accused in the case, including sitting Member of Legislative Assembly V Sivankutty.