The sixth accused, E P Jayarajan, did not appear in court.
The suspects in the stone pelting at the CPM's Thiruvananthapuram district committee office are linked to the students' organisation of RSS.
Jayarajan was shot on his throat while he was travelling by train in Andhra Pradesh in 1995.
Police had also booked the Youth Congress workers and K S Sabarinathan, who had allegedly conspired, on similar charges.
Being miffed at a particular airline may not be that easy for those travelling from the Kannur international airport for there aren't that many options to choose from.
The court order came a day after Chief Minister Pinarayi Vijayan told the Kerala assembly that there was no need to take any legal action against Jayarajan over the incident.
Jayarajan had recently urged people to use trains and boycott Indigo Airlines after the firm imposed a three-week ban on him
The airline had imposed a three-week flight ban on LDF convener EP Jayarajan on Monday.
The prosecution's demand for custody of the former MLA was turned down by the Vanchiyur Principal Sessions Court.
Chief Minister Pinarayi Vijayan ruled out any legal action against LDF convener E P Jayarajan for the alleged assault on Youth Congress members inside an IndiGo flight on June 13.