The police suspect something unusual had happened at the flat on the day before Vaiga's body was found in the Muttar River.
The death of Abdul Azeez, 15, was earlier investigated twice and concluded as a case of suicide, but a re-investigation was launched after a recently circulated video clip suggested foul play.
The interior design contractor was under threat from contract gangs.
Sanu Mohan had dropped his wife off at a relatives place in Alappuzha on March 20, and left with daughter Vaiga before going incommunicado. Vaiga’s body was found in the river the next day.
The crime took place on Tuesday night after Arun reached the house where Anju lived on learning that Sreeju too was there.
Police said the accused had assaulted and bludgeoned their victim after the latter repeatedly refused to withdraw an assault case.
Rao has been in custody since August 28, 2018, awaiting trial in the case.
Jayamadhavan was found dead on April 2, 2017. The district Crime Branch has slapped murder charges in the case.
The action is based on the report of the judicial commission which probed the custodial death.
The court issued the directive while considering a Public Interest Litigation filed by film director Pauly Vadakkan seeking action against web portals promoting online rummy.