Rustam Makhmudov, 37, was arrested by police and military forces at his family home in the Chechen village of Achkhoi-Martan, The Moscow Times reported Wednesday.
Makhmudov has been traveling freely between Belgium and Russia for nearly five years despite being on an international watch list, a Chechen police spokesman told the Times.
Politkovskaya, 48, was shot in the head October 7, 2006, as she returned to her central Moscow apartment from a trip to the grocery store.
The mastermind of her slaying remains unknown and her family has expressed doubt the arrest of the suspected trigger man would shed any light on who actually ordered her death.
The Russian Investigative Committee said law enforcement agencies in Belgium contributed to Makhmudov's arrest, the official Russian news agency RIA Novosti reported.