The finding would appear to further incriminate the Makhmudov brothers, three of 10 suspects that the Prosecutor General's Office said it detained last year.
Prosecutors have not released any names, but several media outlets, including Tvoi Den, have published the list.
Politkovskaya, who wrote articles and books describing brutal actions of government troops in Chechnya, among other things, was gunned down in her apartment building in central Moscow in October 2006.
Colleagues at Novaya Gazeta, which is running a parallel investigation, have slammed the publication of the suspects' identities as a deliberate attempt to sabotage it, and they viewed Wednesday's news in a similar light.
"I'm not going to comment on any publications in that newspaper," said Sergei Sokolov, Novaya Gazeta's deputy editor.
The Tvoi Den report did not cite any sources for the information.
Sokolov said he expected the case to split in two when it goes to court, with one trial for those suspected of carrying out the killing and a second for the suspected mastermind.
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