For months, the most prominent example of this shift has been the push to extradite Inocente Orlando Montano Morales, a former vice minister of defense accused of participating in the meeting where the order was given to kill the Rev. Ignacio Ellacuría, the rector of the José Simeón Cañas University of Central America, and to leave no witnesses alive. The officers believed that Father Ellacuría, who was trying to help broker peace, was an intellectual leader of the leftist guerrillas with the Farabundo Martí National Liberation Front, or F.M.L.N.

The Justice Department is now pressing for Mr. Montano, who is in American custody after immigration violations, to be extradited to Spain, where he and 19 other former officers have been charged with murder and terrorism in the massacre. Five of the six priests were Spanish citizens.

“The U.S. government has moved from an era in which we help provide visas to resettle the Salvadoran military in the United States to an era in which we are supporting their deportation and extradition for criminal charges,” said Geoff Thale, program director of the Washington Office on Latin America and a longtime El Salvador observer. “That’s a really significant shift.”

Mr. Montano, who was living in Massachusetts and was arrested by federal officials in 2011, is the only defendant in custody. At an Aug. 19 hearing, the judge in the case said she would most likely issue a ruling on the extradition request in the coming weeks. If Mr. Montano is sent to Spain, other defendants can be tried with him in absentia.

Those familiar with the case against Mr. Montano say it began as a result of efforts by human rights advocates and a specialized unit of the Justice Department, the Human Rights and Special Prosecutions Section, as opposed to a directive from higher levels of government. But, they add, it would not have gotten this far without support from the top.