
The court also acknowledged that an initial confession from one of the three defendants had been beaten out of him while in custody.
Police had accused Ilyas Malee, 42, Paosi Sateng, 30, and Ya Ah-dae, 61, of taking part in separatist activities from 1999 to 2002.
Ilyas and Paosi both died while in custody.
The police had accused the three suspects of taking part in meetings with members of the Patani United Liberation Organisation, Barisan Revolusi Nasional and other mujahideen groups behind the violence in the Malay-speaking region.
Police also accused them of promoting separatist ideology, as well as carrying out armed activities against state officials.
However, the court's statement said the only witness for the police was not credible. He was identified as Mala Sem, an official of the tambon administration organisation in Yala's Lam Mai.
The court took into consideration the possibility of a personal conflict between Mala and Ilyas, saying the latter was a local imam while the official had been accused of involvement in illegal activities in the area.