The bodies of Zarema Sadulayeva, of the Let's Save the Generation charity, and her husband were found near the Chechen capital, Grozny.
Armed men seized the two on Monday from the offices of Ms Sadulayeva's charity.
The case follows last month's abduction and killing of prominent human rights activist Natalia Estemirova.
On Tuesday, Memorial's Alexander Cherkasov was quoted as saying Ms Sadulayeva's body and that of her husband, Alik Dzhibrailov, had been found in Grozny's Chernorechye suburb.
Let's Save the Generation supports children affected by violence in war-torn Chechnya.