Filiberto Ojeda Rios, 72, fired on the agents Friday from a farmhouse in the western Puerto Rican town of Hormigueros, wounding an agent, said Luis Fraticelli, the special agent in charge of the FBI for the U.S. island territory.
"He opened the front door of his house and opened fire on the agents," Fraticelli said at a news conference amid protests from pro-independence Puerto Ricans who accused the FBI of mishandling the arrest.
"We went to arrest him but when the gunfire started we had to defend ourselves," he said.
The agents waited until midday Saturday to enter the farmhouse because they were unsure if there were explosives inside, Fratecelli said. The agents, who had been staking out the farmhouse for four days, waited for team trained in detecting explosives to arrive from Virginia.
Fraticelli said the FBI tried to persuade Ojeda Rios to surrender but negotiations fell apart. He said the nationalist had demanded that a reporter be present, but the FBI refused, fearing the journalist could be taken hostage.
The armored car robbery of 22 years ago is considered an act of domestic terrorism because the money was used to fund activities by the Puerto Rican nationalist Macheteros, or Cane Cutters. Only about $80,000 of the $7 million has been recovered.
Ojeda Rios had been on the run since 1990 when he cut off an electronic monitoring bracelet and went into hiding while awaiting trial for the robbery of $7.2 million of the Wells Fargo depot in West Hartford, Conn.
A hero in the independence movement, Ojeda Rios was convicted in absentia in 1992 on charges of robbery, conspiracy and transportation of stolen money and sentenced to 55 years in prison.
The FBI agents also arrested Ojeda Rios' wife, Elma Rosado Barbosa, who was unharmed. She was released without charge Saturday evening from a federal prison outside the capital of San Juan, said her lawyer, Julio Fontanet.
The United States seized Puerto Rico in the Spanish-American War. Puerto Ricans are U.S. citizens but cannot vote for U.S. president, have no voting representation in the U.S. Congress and pay no federal taxes.
Most Puerto Ricans are split between those who support making the island a U.S. state and those who favor keeping its status as a U.S. commonwealth. A small but vocal minority supports independence.
Puerto Ricans who have argued for decades about their island's relationship with the United States were unified in criticizing the FBI's handling of the arrest.
"I always said that when they went to arrest him, they would have to kill him," said Juan Mari Bras, a veteran independence leader.
Independence Party President Ruben Berrios, a critic of the violent tactics of the Macheteros, called Ojeda Rios' death "shameful."
Puerto Rico Gov. Anibal Acevedo Vila, who supports keeping the island's status as a U.S. Commonweatlh, criticized the FBI for refusing to provide information about Ojeda Rios' fate until Saturday evening. He said Puerto Rican authorities would investigate whether his death could have been prevented.
The Macheteros have been largely inactive for more than a decade. The group also claimed credit for the 1981 bombing of 11 military planes at a U.S. National Guard base in Puerto Rico. Two marines were killed.
Ojeda Rios was one of four men still wanted for the robbery.
In hiding, the grey-bearded Ojeda Rios sometimes granted interviews to Puerto Rican reporters, always wearing a traditional Caribbean guayabera shirt. He died on the anniversary of a brief 1868 rebellion against Spanish colonial rule in the western town of Lares. Ojeda Rios traditionally distributed a recorded speech to mark the anniversary.
"It's not a coincidence," said Hector Pesquera, the president of the Hostosiano independence movement. "They chose the moment, the date and the political circumstances to carry out this assassination."