Estemirova, a 50-year-old single mother, was found dead in the city of Nazran in Ingushetia, which neighbours Chechnya in Russia' volatile Caucasus region, on July 15.
Her body, which was found with two shot wounds to the head, was discovered just hours after she was seized from her home in Grozny, the Chechen capital.
Orlov, in a posting on Memorial's website after her body was found, had said: "I know, I am sure of it, who is guilty for the murder of Natalya ... His name is Ramzan Kadyrov".
But Kadyrov denied any involvement, and said he would oversee the investigation into her killing.
The Chechen president did not appear in court on Friday, but Andrei Krasnenkov, his lawyer, said Orlov's comments were destabilising Chechnya.
Chechnya and other parts of the Russian Caucasus remain the site of a deadly insurgency led by Muslim fighters against the pro-Kremlin local authorities, who in turn have been accused of human rights abuses.
Security forces are being killed in clashes with fighters on an almost daily basis.
Ongoing attacks against human rights activists has led Memorial and other human rights organisations to suspend their operations in Chechnya.