Speaking to reporters outside the court, Wa Lone said he and Kyaw Soe Oo had committed no crime and would testify to their innocence in court.
The reporters appear in court and are remanded in custody.
The reporters have told relatives they were arrested nearly immediately after being handed some rolled up papers at a restaurant in northern Yangon by two policemen they had not met before.
During pre-trial hearings the prosecution argued the reporters tried to access "secret papers" about security forces and therefore deserved punishment.
On the same day, the military says its soldiers murdered 10 captured Muslims, whose bodies were those discovered by security forces in the mass grave in Rakhine, during insurgent attacks. They said the journalists were arrested in a sting operation by the police that was aimed at interfering with their reporting. At the time, there were many unconfirmed reports that they had been handed incriminating documents at the official's house, and then immediately arrested right after.
Yet the arrest failed to quash their story, which Reuters eventually published as a special report in February.
Former U.S. Secretary of State Rex Tillerson has said the crackdown "constitutes ethnic cleansing" while the United Nations rights envoy to Myanmar said the campaign bears "the hallmarks of genocide".
"We will face the court and are not shaken by the decision to charge us with the secrets act", Wa Lone said after the hearing.
In March prominent rights lawyer Amal Clooney, the wife of actor George Clooney, joined the Reuters legal team to add weight and profile to their defence.
"We are deeply disappointed that the court declined to end this protracted and baseless proceeding", Reuters editor-in-chief Stephen J. Adler said in a statement.
In April, Police Captain Moe Yan Naing testified that a senior officer had ordered his subordinates to plant secret documents on Wa Lone to "trap" the reporter. After giving his surprise testimony, he was jailed for violating the Police Disciplinary Act and his family was forced to vacate their police housing unit.
"Today's decision casts serious doubt on Myanmar's commitment to press freedom and the rule of law", it said.
According to their defense lawyer, U Khin Maung Zaw, the judge said that, "Ko Wa Lone and Ko Kyaw Soe Oo were caught with state information on that day and which stated that they collected and noted down secret government information, either to share with the enemy or to use against the interests of the government by possessing or distributing them".
He said during the "informal" meeting, both Bangladesh and Myanmar have agreed that they should try to improve the situation in the Rakhine State in three steps - to stop violence, to start repatriation as soon as possible and to promote local development. Senator John McCain has called for the release of Wa Lone and Kyaw Soe Oo, saying the charges against the two journalists are "outrageous and politically motivated".
The judge chose to proceed to trial despite strong evidence for dismissal - witness accounts pointing to entrapment, indications of police misconduct in the investigation, and prosecution witnesses with contradicting testimonies.
Detained Myanmar journalist Wa Lone (L) speaks to reporters as he is escorted by police from a courthouse following his ongoing pre-trial hearing in Yangon on July 9, 2018.