Estemirova was found dead on Wednesday afternoon with gunshot wounds to the head and chest, hours after she was seen being bundled into a car outside her home in Grozny, the Chechen capital.
Estemirova was one of Memorial's main employees in Chechnya and had won worldwide acclaim for uncovering rights abuses.
Her death prompted tributes from around the globe and calls on Russia to find the killers.
Oleg Orlov, who heads Memorial, accused Ramzan Kadyrov, Chechnya's pro-Kremlin leader, of being responsible for the murder, saying he was guilty irrespective of who ordered the killing.
Kadyrov's lawyer responded by saying he was suing Orlov for defamation in order to protect the "honour, worthiness and professional reputation of the president of the Chechen Republic".
Kadyrov had earlier personally telephoned Orlov to rebuke him for his allegations.
"You are not a prosecutor or a judge therefore your claims about my guilt are not ethical, to put it mildly, and are insulting to me," the Chechen strongman told Orlov, according to an account of the conversation posted on Kadyrov's website.
"I am sure that you have to think about my rights before declaring for everyone to hear that I am guilty of Estemirova's death," he said.
Orlov had said in a statement, "I know, I am sure who is guilty of Natalia Estemirova's murder, we all know him - his name is Ramzan Kadyrov."
"We do not know if he gave the order himself or his close associates did so to please their boss," Orlov said.
Kadyrov is a controversial figure, praised by the Kremlin for restoring some stability to Chechnya but hated by rights activists, who accuse him of letting his personal security force carry out kidnappings and torture.
In April, Russia ended its controversial "anti-terror operation" in Chechnya, a move that analysts said gave the maverick leader a freer hand in running the region.