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With its neat rows of classrooms and its white domed mosque glowing against a backdrop of misty hills, the Hidayatullah Islamic school on the Indonesian island of Sulawesi seems the very picture of peace. "Yes," smiles Nyupeno, a school administrator, "it's quite cozy here."

But Nyupeno's smile quickly disappears when he is asked about some of the people who have allegedly passed through the school: suspected members of Jemaah Islamiah (JI), the Southeast Asian network of Muslim militants blamed for numerous bombings region-wide, including the October 2002 attack in Bali that claimed 202 lives. Nyupeno flatly denies police allegations that a convicted Bali bomber, Ali Imron, had once taken refuge in one of the spartan cubicles at the rear of the mosque where the staff sleep. He also rebuts claims made by another bombing suspect during police interrogation that the school was used as a way station by militants traveling to and from the island of Mindanao in the southern Philippines for combat training. No, says Nyupeno, he has never heard of Suryadi Mas'ud, currently imprisoned for involvement in several bombings in the south Sulawesi city of Makassar in December 2002. Suryadi told police he spent several years guiding militants from a JI-affiliated group in Makassar to Mindanao, and in mid-2001 spent a month living at the school along with several of his charges while awaiting transport.

The strict secrecy practiced by JI and its affiliates means that Nyupeno and many other teachers might have had no idea of the true identity of the travelers who took advantage of the school's hospitality. (A teacher at the school, whom police allege has links to JI, disappeared in November last year.) Indeed, one of JI's greatest strengths is that its cells function as independent, clandestine units with scant knowledge of the rest of the organization. After his arrest in April, one top JI militant, Mohamad Nasir bin Abas, explained to police, "There can be members of JI who don't even know the name of the emir [leader]. They don't even know the name of the organization."

But as more and more senior JI members are arrested and questioned, and the organization's internal documents come to light, some of the veils of secrecy are being stripped away. Recent interrogation and intelligence reports obtained by TIME make it clear that one of JI's best-kept secrets is the ambitious scale of its training camps in Mindanao, which has replaced Afghanistan as the preferred location for learning how to wage terror. Even more alarming: more than a year after Bali, both the camps and the supply routes for recruits appear to be functioning normally.

According to a source close to the police investigations who has reviewed the bulk of seized JI documents, the organization's own accounting shows that some 3,000 trainees have passed through Mindanao since the mid-1990s. A recent intelligence report prepared by the Philippine military and seen by TIME estimates that 600 JI members are currently in Mindanao, scattered among at least three camps. That figure, contained in a so-called Jemaah Islamiah situationer dated Dec. 8, includes an unspecified number of Filipinos, but the bulk of trainees are believed to be Indonesians, along with some Malaysians. The report, which details the location of the three camps and a number of JI "safe houses" in Mindanao and Manila, contradicts last week's relatively reassuring assertion by Defense Minister Eduardo Ermita that there are only 31 JI members active in Mindanao.

President Gloria Macapagal Arroyo's National Security Adviser, Roilo Golez, emphatically denies that 600 JI members are present in the Philippines. "That's wrong," he tells TIME. "Very, very wrong. I can bet my future, my career and my life that it's not true." The government has made similar assertions in the past. Arroyo herself denied for months that the JI problem was serious. Then in an about-face in November, she announced that her administration now regards JI as the country's biggest national security threat.

As Ermita himself has noted, Manila is in a delicate position when it comes to JI. The government is still attempting to negotiate a cease-fire with the Moro Islamic Liberation Front (MILF), whose 12,000 guerrillas are fighting to gain autonomy for sections of Mindanao. In earlier peace talks, the MILF foreswore any contact with JI, and its leaders say they will help Manila hunt down the group's members if they seek sanctuary within MILF territory.

According to the Dec. 8 intelligence report, however, many MILF guerrillas are actually training inside the JI camps, one of which is said to be guarded by 150 MILF regulars. That information jibes with details provided by Taufik Rifki, also spelled Taufek Refke, an alleged JI trainer at a camp the Dec. 8 report confirms is located on Mount Cararao in Mindanao's southwest. Rifki, a 29-year-old Indonesian who was captured on Oct. 2, gave Philippine police a detailed description of the JI camp where he was stationed. He said the camp was guarded by MILF fighters from the Iranon tribe and named several MILF contacts who he claimed provide financial and other support to JI. For its part, the MILF has long maintained that it has no knowledge of or contact with foreign terrorist organizations. "We have nothing to do with the JI," says Eid Kabalu, MILF spokesman.

With its detailed description of a long-established and meticulously organized training camp deep in MILF territory, Rifki's interrogation throws serious doubt on that assertion. Among the documents seized by Philippine police when they captured Rifki were printed grading sheets that listed the names of cadets and the scores they achieved at various stages of their training. Rifki also gave police a breakdown of the courses most recruits underwent—ranging from a basic four-month stint to two years for potential instructors. All cadets received training in infantry tactics, weaponry (everything from pistols to automatic rifles, light machine guns, mortars and rocket-propelled grenades), map reading and explosives. Rifki told police that the explosives section included "actual samples of TNT, black powder, PETN, ammonium nitrate and C4. Students also worked with detonators, detonating cords, blasting caps and timing devices (alarm clocks). Practical exercises were conducted with 100 grams of explosive material." In addition, states the Dec. 8 report, cadets studied Islam intensively, receiving up to four hours a day of religious indoctrination "required to produce suicide bombers."

There are plenty of young Muslims eager to join up. Many see the global war on terror as an attempt by the West (specifically the U.S.) to crush Islam. Jihad can also provide an escape to those mired in poverty. "Even if a fraction of 1% of [Indonesia's] population is predisposed to extremism, that's a huge number," says Ken Conboy, author of Intel: Inside Indonesia's Intelligence Service. That makes blocking the pipeline to Mindanao critical. Though Malaysian, Indonesian and Philippine police all say they have stepped up patrols between Indonesia and the Philippines, their efforts don't seem to have stemmed the flow of would-be cadets. When Rifki was captured, he was waiting in a hotel in the Mindanao city of Cotabato for a batch of 10 newly arrived Indonesian recruits to join him for escort to the camps.

Regional intelligence officials say that because of JI's amorphous, compartmentalized structure (modeled on its mentor organization al-Qaeda), even the arrests of many of its leaders in the past 18 months won't cripple it, particularly as long as the pipeline of men and weapons to and from the southern Philippines remains open. "While there's enough command and control to get people to the Mindanao camps, JI is very much alive," says Zachary Abuza, author of the book Militant Islam in Southeast Asia. "Even if you manage to catch the top 10 most-wanted JI guys still on the run, you've still got a huge problem on your hands. Small fish eventually grow up to be big fish, and you've got a whole sea of fish out there."

• Simon Elegant | Jakarta
• Secret reports obtained by TIME reveal startling details of how Jemaah Islamiah is regrouping