Lawyers for the three defendants and for Politkovskaya's family had pressed for the trial to be opened up to public scrutiny, saying that that was the only way to ensure justice was done in the politically charged case.
"It is simply outrageous that they [the jurors] didn't even come out into the court room," Said Arsamirzayev, a lawyer for one of the accused, said.
"We have all been treated like little kids: We were shown the candy and promised a fair and open trial, but now we understand it is not going to be the case and we will have closed hearings," he said.
Politkovskaya, aged 48 when she died, was a writer of books and articles that fiercely criticised Putin, notably for abuses committed by Russian forces during the second Chechen war, which took place under his watch.
Her killing, as she returned home carrying bags of groceries from a shopping trip, sparked outrage internationally and among opposition groups in Russia, with some critics pointing the finger of blame at the Russian leadership.