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In Chile, the first case to implicate the Catholic Church clergy in the repression carried out by the late dictator, Augusto Pinochet, is unfolding. A priest who served as a military chaplain is accused of helping cover up the executions of political prisoners in Chile's northern region shortly after Pinochet seized power in the 1973 coup that ousted President Salvador Allende.

NPR's Julie McCarthy has this report.

JULIE McCARTHY: The baked plain of the Atacama Desert in northern Chile holds many secrets.

Ms. GRIMILDA SANCHEZ(ph) (Resident, Chile): (Spanish spoken)

McCARTHY: Some of them lie in the collection of old documents that 79-year-old Grimilda Sanchez combs through at her kitchen table. In 1973, Grimilda lived in the Atacama Desert town of Calama. The desolate mining region had been a stronghold of socialist President Salvador Allende. And Grimilda's family -ardent Allende supporters.

From the stack of aging papers, she retrieves the death certificate of her husband, Luis(ph), taken into custody after Allende was ousted by Pinochet in September 1973. It says Luis was killed by gunfire to the chest in Calama in October '73. It was the same story military chaplain and Catholic priest Luis Jorquera Molina gave Grimilda when he visited her at the Calama Prison where she had just been taken.

Father Jorquera told her that her husband was shot trying to escape his jailers.

Ms. SANCHEZ: (Spanish spoken)

McCARTHY: The priest appeared to be innocent. Why? Because he brought a message from my husband saying, you are very sick, Grimilda, and you should leave the country. I wasn't sick, she says. And the priest didn't know that my husband was secretly telling me they had terrible accusations against me, and to save myself, I should leave.

But Grimilda soon began to suspect that the priest was involved in the government's anti-Allende crackdown. Father Jorquera returned to Grimilda just 13 days later to say that her son had been killed.

Ms. SANCHEZ: (Spanish spoken)

McCARTHY: I wanted to kill him, she says, her gold earrings bobbing as she reenacts the story. I grabbed him by the lapels and said, what are you doing? What are you, a priest, doing in those military clothes? Don't we have rights? Don't we even have human rights? I was overwrought. I'd lost my husband on the 6th of October, and my son on the 19th. The priest fled screaming saying, I was possessed, she says.

Grimilda's 25-year-old son was one of 26 people killed in Calama by the infamous Caravan of Death. The squad swooped in on military helicopters with orders to eliminate subversives in the Atacama Desert region. The killings occurred just weeks after Pinochet overthrew President Salvador Allende. Being backers of Allende, Grimilda and her son were rounded up and tortured.

Ms. SANCHEZ: (Foreign language spoken)

McCARTHY: The hearing is bad in both my ears. They destroyed my nipples where they put electric charges on them and in my rectum. And my son, they pulled out his fingernails and toenails. I stood on a tabletop to look through a window. It was October 19th, and I saw the Caravan of Death pull up with a list. They took 26 people away including my son, she says.

Now, 34 years after the fact, Father Jorquera and 12 other military men have been named in a case alleging that they covered up the killings carried out by the Caravan of Death.

Attorney Eduardo Contreras, who represents families of the victims, alleges that as Chaplain Jorquera was consoling surviving relatives, he was also aiding the military's crimes.

Mr. EDUARDO CONTRERAS (Lawyer, Chile): (Through translator) On the night of October 19, 1973, he was in Calama when the Caravan of Death arrived. The priest accompanied the firing squad to a hill and witnessed the execution of the 26 prisoners - the cutting up of some of their bodies, the burial of their remains.

McCARTHY: Father Jorquera denies participating in the executions. The cover-up he's implicated in took place several years later when the government grew nervous that the truth about its campaign of killings would be exposed. Pinochet's regime had disposed of dissidents by throwing some of them out of aircraft over the Pacific Ocean.

Attorney Contreras says when the body of a political prisoner washed up along the coast in 1976, the conspiracy to hide the massacre in Calama was hatched.

Mr. CONTRERAS: (Through translator) At that moment, Pinochet gave the order that corpses should be dug up and disposed of more thoroughly. Calama is not far from the ocean so some were thrown into the sea, but in the interior bodies were sprinkled with gasoline, put on a big grill and incinerated.

McCARTHY: Until a few weeks ago, Father Jorquera celebrated mass in a quiet parish in Chile's capital, Santiago. As investigators closed in, he entered a military hospital denying any wrongdoing.

Father Sergio Zanartu is the former director of the Jesuit magazine Mensaje, or message, the first to suggest that basic rights were being abused under the dictatorship. He says there were tense debates at the time inside the clergy about the role of military chaplains. A few of whom, he says, broke their vows.

Father SERGIO ZANARTU (Former Director, Mensaje Magazine): (Through translator) A chaplain has a military rank, and the highest rank he can have is a general. They began to take on the colors of the military and in this way, some internalized the armed forces and its reasoning, and belongs more to the military than to the church.

McCARTHY: I asked Father Zanartu what obligation the church owed to the victims today.

Should the church apologize? Should the church say we're sorry what was done by our people? It's a black mark on the church.

Fr. ZANARTU: (Through translator) The support of Chile's Catholic Church in defense of human rights was so massive that I don't think it's necessary to apologize. For an exception, there's always exceptions. If the church had not acted so strongly, then, yes, we should have apologized. Nobody asked the church to do so. That's not the case in other countries where the role of the church was not clear.

McCARTHY: The Supreme Court in Chile recently overturned the indictments against the 13 defendants, including Farther Jorquera for alleged cover-up conspiracies in Calama. The high court ruled that a lower court had overreached in its findings.

State attorneys battling on behalf of relatives of the victims call it a setback, but not the end. The government, meanwhile, has not dropped charges against Grimilda Sanchez for illegally exhuming her murdered husband nearly three decades ago.

But only then she says that she learned of the lie in the death certificate that he'd been shot in the chest.

Ms. SANCHEZ: (Spanish spoken)

McCARTHY: I removed the army blanket and looked, but there was no sign of gunshots on his chest, nothing. When I turned him over, I found a huge wound on his tailbone. I realized then, she says, that he'd been terribly tortured.

Grimilda says it is not for her to pass judgment on Father Jorquera, but she adds…

Ms. SANCHEZ: (Spanish spoken)

McCARTHY: I believe that every person must answer for what they've done. He was also a priest and had a moral obligation to look after people. The church teaches that to have humanity and he, she says, did not have it.

Julie McCarthy, NPR News, Santiago, Chile.

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