The court turned down prosecutors' request to hold the trial in a closed court. The prosecution had said that material due to be presented as evidence during the trial included classified documents.
Defense lawyers acting for the suspects and the journalist's family had insisted on an open trial.
"A closed trial could lead to negative consequences," a lawyer of one of the suspects said adding there were only a few classified documents in the case files, which were unlikely to be read out at the trial.
The presiding judge said, however, the trial would be held in a closed court "if jury members are reported to come under pressure." The court is expected to select a jury for the trial on Tuesday.
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.
A lawyer acting for the Politkovskaya family urged in the courtroom on Monday further investigation into the murder.
"We want to see all those involved in the defendants' cage, but at the moment the main suspects are not in the courtroom," Karina Moskalenko said.
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.
Since the fall of the Soviet Union in 1991, Russia has been one of the most dangerous countries for reporters, according to international groups. The Committee to Protect Journalists says 49 media professionals have been confirmed killed in Russia since 1992. Only Iraq and Algeria have had more deaths over that time.
The murdered journalist's children said on Monday they had filed a plea for 10 million rubles ($366,000) in compensation. The judge accepted the plea.