Jane Perlez, Jakarta – Indonesia's top military and police generals took control of the provincial capital of Jayapura in Papua on Friday, ordering the arrests of university students and directing the riot police to fire into the air as they patrolled the streets.

Nearly 60 people, many of them students at Cenderawaih University, have been arrested in connection with a violent demonstration Thursday that resulted in the death of three policemen and an air force officer, a police spokesman, General Anton Bachrul, said.

The protest, organized against the American mining company Freeport-McMoRan, which operates a huge gold and copper mine about 500 kilometers, or 300 miles, from Jayapura, turned violent when the police clashed with several hundred students near the campus.

After the policemen and the military officer were killed, the police started shooting, a former policeman and security officer for the mining company said Friday. "It was extraordinary that the police did not kill anyone, they were so mad," the former policeman, who declined to be identified, said.

In an unusual display of strength and in a reflection of the seriousness of the violence, the Indonesian Army chief, General Djoko Suyanto; the head of the police, General Sutanto; and the head of the domestic intelligence service, Syamsir Siregar, arrived in Papua on Thursday night.

The sudden show of Indonesian military brass in Papua, the country's easternmost and poorest province, was not only to protect the valuable mining company, but the country's hold on the province itself.

A low-level insurgency has rumbled for decades against the central government, and the student protesters openly sympathize with it.

The sounds of shooting reverberated Friday from the area of Adepura, around the university, and schools and markets were closed, residents of Jayapura said.

The riot police officers from Brimob, the most feared of Indonesia's police units, were still going door to door at the university dormitories, said Hans Magal, the secretary general of the Highland Students Association.

The police were targeting students from the highland region where the mine operates, Magal said by telephone from Timika, the town adjacent to the mine.

The violence directed against Freeport, an escalation of scattered incidents in the past month, is the most severe against the company since Papuans armed with bows and arrows rioted at the mine site 10 years ago.

The current protests began last month and operations were closed for three days. They then spread to Timika and the provincial capital.

To quiet the antagonism after the 1996 rampage, the company began directly paying individual police and military officers to protect the mining operations that stretch from glacier-capped mountains to the coastal lowlands, where the mine waste covers 230 square kilometers, or 90 square miles, of former wetlands.

The New York Times reported in December that Freeport had granted far greater financial support to the Indonesian Army and police in Papua than the company had publicly reported, in some cases giving individual commanders tens of thousands of dollars.

The 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 told the New York City Pension Fund, a major investor in Freeport, that it was also investigating if the company failed to fully disclose the payments to its shareholders.

After the 1996 riots, the company paid for new social programs for local people, assigning 1 percent of annual revenues for medical services, schools, roads, and AIDS programs.

Whether, or how, the New Orleans-based company and the Indonesian government can make such a relatively quick fix to tame the current surge of anger is an open question.

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 Friday 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, the company announced record profits in the final quarter last year, as gold prices reached a 25-year high.

Beanal said by telephone from his home in Timika that he had advised Freeport recently that to reduce hostilities toward the mine, the company needed to deal more effectively with more than 700,000 tons of daily mine waste.

Protests against the mine began last month when villagers were told by the security forces that they could no longer pan for gold in the waste.