Their lawyers demanded the presiding judge be replaced, arguing that he cannot be impartial because of a separate case that pits him against one of the journalists.
The case is seen as a test for media freedoms in Turkey, but the lawyers' demand could bring a quick end to the opening hearing if the court decides to adjourn the trial until a ruling by a higher court over whether to replace the presiding judge, Resul Çakır, state-run TRT television reported.
Çakır was a plaintiff in a case against one of the defendants, Barış Terkoğlu of the anti-government news website Oda TV, over the publishing of a photograph that showed Çakır and some other judges joining senior police officials at a fast breaking dinner at a police headquarters in 2009 to suggest cozy relations between them.
Thirteen defendants, including investigative journalists Nedim Lener and Ahmet Şık and writer Yalçın Küçük - a staunch government critic, went on trial Tuesday. Among them also was Soner Yalçın, the owner of the Oda TV. A key suspect, an intelligence official, recently died of a heart attack in jail.
International media rights groups who traveled to Turkey to attend the trial warned the government that the level of press freedoms serve as a barometer for democracy in a country.
"We want to express our solidarity with our detained colleagues but in the meantime express our concern for press freedom in Turkey," Philippe Leruth, vice president of the European Federation of Journalists, told AP television outside the court house in İstanbul. "Because press freedom is essential for democracy."
Journalists unfurled a banner in support of their colleagues that read: "Turkey set journalists free."
"Jailing journalists for their opinion is really not acceptable in democratic countries," Pavol Mudry, a member of the executive board of the International Press Institute said. "Therefore we are here to support these journalists."
The suspects are among some 400 people on trial in an investigation - now in its fourth year - into an alleged hardline secularist group which allegedly plotted in 2003 to bring down the government through attacks that prosecutors say would have created chaos and sparked a military coup.
Prosecutors accuse the journalists of being members of the media wing of the alleged Ergenekon group, which authorities described as an armed terrorist organization, and working to manipulate public opinion.
Other suspects in the case include politicians, academics and retired military officers.
Critics say the trial is based on flimsy or fabricated evidence and aims to intimidate and muzzle government opponents. The government insists the journalists are not jailed for their writings but for alleged criminal activity.