"The defendants said they have nothing to hide and will give all necessary evidence," Murad Musayev said, adding that 98% of the indictment consists of "conjectures and assumptions."
The trial, which began on Wednesday, is being held in a closed court after the jury refused to appear in a courtroom in the presence of journalists.
Politkovskaya, who gained international recognition for her criticism of the Kremlin and reports of military atrocities against civilians in the troubled Caucasus republic of Chechnya, was gunned down in an elevator in her Moscow apartment building in what police described as a contract killing.
Three men, a former police officer and two brothers from Chechnya, have been charged with involvement in the murder. Sergei Khadzhikurbanov and Dzhabrail and Ibragim Makhmudov have been in custody since last August. Investigators have provided no details as to their alleged roles in the crime.
The man suspected of pulling the trigger, Rustam Makhmudov - the eldest of the Makhmudov brothers - remains at large. A separate case has been launched against him. It is still unknown who was behind the killing.
A former Federal Security Service (FSB) officer, Colonel Pavel Ryaguzov, has also been charged with abuse of office after allegedly telling the killers where Politkovskaya lived.