Two of the three men, arrested in the provincial capital Banda Aceh on May 17 as they were leaving the province for peace talks in Tokyo, face the death penalty. The other faces life imprisonment. All appeared in separate court sessions.
Prosecutors said two of the men had provided help to the Free Aceh Movement (GAM) fighters in carrying out their attacks in the past few years. The third had failed to prevent attacks being carried out by GAM when he knew of them in advance, the prosecution said.
All three had committed treason by trying to "separate Aceh from Indonesia", the prosecutors added.
Defendant Teuku Muhammad bin Usman denied the charges against him and said negotiating for peace was a noble thing to do.
"Many charges were inappropriately applied to us. Our noble task as negotiators has been called a malicious conspiracy," Usman told the court, secured by more than 30 policemen and packed with journalists.
Usman's trial and that of co-defendant Teuku Kamaruzaman were adjourned until August 5. The trial of the third defendant Amni bin Ahmad Marzuki, who faces life in jail, was adjourned until August 4.
Defence lawyer Rufriadi said the indictments against all three were confusing.
|"Our noble task as negotiators has been called a malicious conspiracy."|
- Defendant Teuku Muhammad bin Usman
"There is some confusion in the prosecutors' indictment which tries to relate the charges with terrorism. The incidents mentioned in the indictment had no relation to the defendants," Rufriadi said.
Another two rebel negotiators are due to go on trial on Wednesday.
Indonesia launched a massive military offensive in the northwestern province on May 19 after the Tokyo peace talks broke down. More than 500 people, most of them rebels, have been killed in the fighting, the military has said.
GAM, which has sought independence for gas-rich Aceh since 1976, has given a far higher death toll, saying most are civilians and government forces.
More than 10,000 people, most of them civilians, have been killed in the Aceh conflict since 1976.