Problems in the criminal justice system in the South stem from protracted investigation processes and unjust and inefficient investigation procedures, the report said.
This has resulted in inadequate and inappropriate evidence gathering, it said.
The report concluded that these factors resulted in high acquittal rates in security-related lawsuits.
The research paper, titled "The Effectiveness of Prosecution of National Security Charges and the Protection of Citizens Rights: A Case Study of the Four Bordering Provinces in Southern Thailand" was prepared by the Office of the Attorney General Region 9.
The report was spearheaded by veteran prosecutor Sakchai Asawin-anand and sponsored by the Asia Foundation.
Replacing retiring experienced police investigators and public prosecutors with lesser experienced officials _ or not replacing them at all _ coupled with the overlapping works in forensic science agencies, amid a dangerous working environment, have hampered the scientific evidence gathering process, the report said.
The researchers found the legal process for security cases in the far South is protracted.
They cited these examples: 81 days for police to submit a case to the prosecutor; 32 days for the prosecutor to indict the suspects; 461 days for the Court of First Instance to reach a judgement; 424 days for the case to reach the Court of Appeal; and 858 days before the Supreme Court reaches a judgement.
The research also noted that most suspects are denied bail while waiting for police to forward the case to the prosecutor.
A former military task force chief who used to be based in the deep South told the Bangkok Post that he still had to stand as a witness in one lawsuit that entered the court four years ago. During his seven years working in the restive region, he testified in 24 lawsuits.
Agencies have, however, gradually responded to the problems.
Public Prosecution Region 9 director-general Nitsit Rabeabtham said all agencies relating to justice enforcement, including the National Security Council, the Southern Border Provinces Administrative Centre, the Royal Thai Police, and the OAG have improved their coordinations and communications.
"Our policy towards the southernmost provinces is to ensure efficient, fast and cheap justice," Mr Nisit said.
"We also adhere to human rights principles and step up our efforts to contain crime, maintain social order and peace in the region.
"We will make the people confident in the justice system."
Court hearings in the far South will be attended by a deputy court director to help create an atmosphere of trust and fairness throughout the proceedings, Mr Nisit said.
The prosecutor, however, conceded that inadequate evidence _ especially that provided by witnesses and forensics _ was a major obstacle for the judicial process in the deep South.
The OAG will next month open a so-called front-office in Pattani to make legal process quicker and more effective. While security officers invoke Section 21 of the Internal Security Act, which allows suspects in security cases to surrender and undergo a rehabilitation process, to deal with security cases, the OAG would consider expediting its own law that allows it to drop charges for the sake of social and political stability, Mr Nisit said. Since 2008, only three suspects in security cases have been set free after they surrendered.
The OAG research also reveals that between January 2004 and July 2012, police have dealt with 7,918 security cases in Yala, Pattani, Narathiwat and four districts of Songkhla, but only 4,686 cases were forwarded to the OAG and only 907 cases reached court.