Indonesian President Susilo Bambang Yudhoyono signed a decree late on Tuesday granting the amnesty to members of the Free Aceh Movement (GAM), as required under a peace pact signed on 15 August between the government and separatists.
"A total of 74 GAM prisoners were released early this morning and left for Jakarta at around 4am (2100 GMT) on board two buses," said Etty, an official at Sukamiskin jail in Bandung, 200km southeast of the capital.
Etty said the released prisoners were heading for Jakarta's Sukarno-Hatta airport to board a flight home.
In Surabaya, 169 prisoners linked to GAM were freed early on Wednesday and some were already on their way to Jakarta by air, an official at the East Java Justice and Human Rights office said.
The official said the GAM detainees from prisons across the province had been gathered at the Porong state prison and released there early on Wednesday.
The August Helsinki peace agreement is aimed at ending 29 years of separatist conflict in Aceh which has claimed some 15,000 lives.