Chisinau Central district judge Lilia Vasilevici said that the hearings surrounding Pasat, a former Moldovan defense minister and former Information and Security Service director, would be held behind closed doors.
Board member Pavel Smirnov said he did not understand that decision.
Moldovan Prosecutor General's Office representatives insisted on the trial being closed, saying certain episodes of the criminal case were classified.
Pasat was arrested in Chisinau airport on March 11. He is being accused of abusing of authority, which entails grave consequences.
The prosecution said then-Moldovan Defense Minister Pasat had concluded a deal to sell MiG-29 aircraft in 1997, which inflicted $53 million in damages on the state.
Prosecutors say Pasat concluded a deal to sell Uragan salvo-launching systems through a foreign firm at cut-rate prices, resulting in a $1.8 million loss for the state.
Pasat maintains that the case against him is "a political reprisal on the part of Moldovan President Vladimir Voronin."
The Moldovan Prosecutor General's Office denies any political motives in the case.
Hearings are scheduled to continue until July 15, Pasat's lawyer Gheorghe Amihalachioae, said during a break in the session. He declined to comment on a possible outcome in the trial.