JAKARTA, Indonesia , March 17 — Indonesia's top military and police generals took control of the provincial capital of Jayapura in Papua today, ordering the arrests of university students and directing riot police to fire into the air as they patrolled the streets.
Nearly 60 people, many of them students at Cenderawaish University, have been arrested in connection with a violent demonstration Thursday that resulted in the deaths of three policemen and an Air Force officer, a police spokesman, Brig.Gen. Anton Bachrul Alam, said.
The protest organized against the American mining company, Freeport-McMoRan, which operates a huge gold and copper mine about 300 miles from Jayapura, turned violent when riot police, armed with shields, batons and tear gas clashed with several hundred students near the campus.
After the policemen and military officer were killed by rock-throwing students, the police grabbed weapons and started shooting. "It was extraordinary that the police did not kill anyone, they were so mad," said a the former policeman and security officer for the mining company, who declined to be named.
In an unusual display of strength reflecting the seriousness of the situation, Indonesia's army chief, Gen. Djoko Suyanto; the chief of police, General Sutanto, and the head of the domestic intelligence service, Syamsir Siregar, all arrived in Papua Thursday night.
The sudden show of Indonesian military brass in Papua, the nation's easternmost and poorest province, was not only to protect the valuable mining company, but the nation's hold on the province itself. A low level insurgency against the central government has rumbled for decades , and Thursday's student protestors openly sympathize with it.
The sounds of shooting reverberated today from the suburb of Adepura, around the university, and schools and markets were closed, residents of Jayapura said.
Riot police from Brimob, the most feared of Indonesia's police units, were still going door to door at the university dormitories today, said Hans Magal, the secretary general of the Highland Students Association.
The police were targeting students from the highland region where the mine operates, Mr. Magal said in a telephone interview from Timika, the town adjacent to the mine.
The violence directed against Freeport, an escalation of scattered incidents in the last month, is the most severe against the company since Papuans armed with bows and arrows rioted at the mine site 10 years ago and closed down operations for three days.
The current protests began at the mine last month, when the police prevented people who live nearby from panning for gold in the mine's waste that pours down the Aghawagon River, a longtime practice. Operations shut down for three days. The demonstrations then spread to Timika, the nearby town, and finally to Jayapura.
To quiet the local antagonism after the 1996 rampage, the company began directly paying individual police and military officers to protect the mining operations that stretch from 12,000-foot glacier-capped mountains to the coastal lowlands where the mine waste covers a 90 square mile area of former wetlands. It accumulates at a rate of 700,000 tons a day.
The New York Times reported in December that Freeport had granted far greater financial support to the Indonesian army and the police in Papua than the company had publicly reported, in some cases giving individual commanders tens of thousands of dollars.
The United States Justice Department has said it is investigating whether these payments made from 1998 to 2004 were in breach of the Foreign Corrupt Practices Act. The Securities and Exchange Commission, too, told the New York City Pension fund, a major investor in the New Orleans-based Freeport, that it is investigating whether the company failed to fully disclose the payments to its shareholders.
After the 1996 riots, the company also paid for new social programs for the local people, assigning 1 percent of annual revenues for medical services, schools, roads, and AIDS programs.
The most senior Papuan at Freeport, Thom Beanal, a leader of one of the biggest tribal groups, the Amungme, and a director of the Indonesian unit of Freeport, said today that the company was concerned about maintaining its daily operations in the current atmosphere.
Consistently one of the largest sources of income for the Indonesian government, Freeport announced record profits in the final quarter last year, as gold prices reached a 25-year high.
Mr. Beanal said in a telephone interview from his home in Timika that he had advised Freeport this week that in order to reduce hostilities toward the mine, the company needed to deal more effectively with the immense amount of waste that is generated every day.
"I suggested they put the waste in a pipe and put it far away," Mr. Beanal said.
Environmental activists — and some mining engineers — have made similar suggestions to Freeport but the company has rejected them, saying such proposals were too expensive.