The report, obtained by CPI under the Freedom of Information Act, depicted a sort of frat-house atmosphere at the Center. It stated that staff had exchanged “racially charged emails” — including one directed at President Barack Obama; used offensive language such as “faggot,” “buttboy” and “homo”; and that “women employees feel that they are treated inappropriately.” Even senior leaders used “inappropriate hand gestures,” it said, and mentioned simulations of masturbation.

Ospina Ovalle, in a telephone call from his NDU office this week, said he decided late last year to retire from the university when the semester ends in two months, and return to Colombia because — he said — he misses it. He said accusations that the Fourth Brigade played any role in the El Aro massacre were false and that “we’ve been cleared.” He said he only found out about it after the carnage was over, from the head of a battalion under his command.

“The FARC wore the same uniforms as the army, so people would assume that they were the army,” he said. The region that his brigade of roughly 2,000 soldiers patrolled included 125 municipalities, and it was woefully underequipped, he said, so he usually did not have timely intelligence about what was happening in the region.

Colombia’s attorney general looked into the allegations about Ospina in 2001 and did not find proof of the Army’s involvement in the El Aro events. But a report in 2006 by the Inter-American Commission on Human rights, an investigative tribunal affiliated with the 35-nation Organization of American States, concluded that “the participation and acquiescence” of the Colombian Army in the paramilitary actions at El Aro and the theft of livestock by “agents of the state” were demonstrated.

“There is no doubt,” said Adam Isacson, director of the regional security program at the Washington Office on Latin America, an advocacy group, that Ospina Ovalle “did nothing to stop that massacre from happening.” Human Rights Watch and Amnesty International, in reports published in 2000 and 2001, respectively, both cited extensive ties between paramilitaries involved in the El Aro massacre and the Fourth Brigade under Ospina Ovalle’s command. “Among the cases in which Ospina is implicated” is the Oct. 1997 event, the Amnesty report states.

Jim Zackrison, a former intelligence analyst with the U.S. Navy’s Office of Naval Intelligence and scholar at the NDU’s Institute for National Strategic Studies, said to the contrary that in his view, the Colombian had enormous charisma and “was the last guy you would find participating in a massacre.”

Zackrison said he invited Ospina Ovalle to speak to his son’s Boy Scout troop, and that the former Armed Forces commander regaled them with a story about “the time he took a bullet for the president” and an account of military strategy while the boys walked along the Gettysburg trail. He said he recalls Ospina Ovalle telling a classroom of NDU students on another occasion that 90 percent of the time, confessions derived from torture will lead interrogators down false paths.

But human rights officials at the State Department consider these groups’ allegations about Ospina Ovalle’s involvement in the El Aro incident credible, according to multiple sources.

The department looked into Ospina Ovalle’s record after inquiries were made by Leahy, a senior government official said, and has serious concerns about his hiring and the absence of appropriate NDU review beforehand. The official, who spoke on condition he not be identified, said that it seems “there are cases that slip through the cracks” because NDU is not “plugged into a daily conversation” about foreign policy and human rights.

Ospina Ovalle is not the first NDU lecturer to be accused in recent years of involvement in serious human rights abuses.

A former Brigadier in the Chilean Army, Jaime Garcia Covarrubias, taught courses from 2001 until 2013 on security strategy and democratic leadership, according to NDU documents listing him as a professor in the William Perry Center for Hemispheric Defense Studies, named after the former U.S. defense secretary. The Center is considered a teaching arm of the U.S. Southern Command.

An NDU promotional video in Oct. 2011 shows Covarrubias standing before a group of students in a red bow tie and describes him as the teacher of a course in Advanced Civil-Political-Military Relations. Former colleagues described him as part of the school’s inner circle of administrators and faculty members, who held unusual sway over its policymaking.

Internal alarms were initially raised about Garcia Covarrubias by others at NDU in 2008, who cited published allegations that he worked for Chilean dictator Augusto Pinochet’s secret police at a base where prisoners were allegedly murdered. But the school’s administrators undertook no investigation of their own at the time, according to documents and interviews.

Garcia Covarrubias was hired “with the approval and full consultation of the U.S. embassy in Santiago,” said Dennis Caffrey, who was dean of students and administration at the time. He said that to his knowledge, the claims swirling around Garcia Covarrubias are only unproven “accusations.”

Regional press reports in 2010 and 2013 said that Garcia Covarrubias had been accused by prisoners and witnesses of beatings and torture. A former prisoner at Garcia Covarrubias’ regimental base in the southern city of Temuco, Herman Carrasco, told an appeals court there in Sept. 2010 that Covarrubias “forced us to perform naked acts of sodomy, without success,” according to an article published that year by the Spanish news agency EFE.

Finally, in 2013, a Chilean judge indicted Garcia Covarrubias for first-degree murder in 1973 of seven political prisoners at his Temuco base, and barred Garcia Covarrubias from leaving the country. The bodies of the prisoners had been thrown into a river, and Garcia Covarrubias and his colleagues at the base told others they were killed while trying to attack the guards, according to a news report on his indictment by the Chilean newspaper Cooperativa.

At the time of the killings, Washington was tightly allied with the Chilean government. A diplomatic cable several days later to the Secretary of State by a senior U.S. diplomat, Jack B. Kubisch, mentioned the deaths of “seven leftists…on a military post in a Southern city” as a failed “leftist initiative.” Kubisch served as NDU’s vice president from 1977 to 1979, and on an advisory board to its Board of Visitors in 1982, according to a university spokesman. He died in 2007.

The Chilean judge’s 2013 travel prohibition blocked Garcia Covarrubias’ return to NDU, and provoked scattered attention in Western media. When questioned by a reporter at Foreign Policy magazine, an unnamed NDU spokesman effectively disowned him, saying Garcia Covarrubias was technically not “an employee of the National Defense University” but a civilian employee of the Office of the Secretary of Defense “with the Defense Security Cooperation Agency serving as the Executive Agent. His current appointment ends on February 25, 2014.”

Update: On March 27, journalists at the McClatchy newspaper chain published an article stating that the State Department revoked Covarrubias’ visa in June 2011, one and a half years before he was detained in Chile and a Chilean judge denied him permission to return to the United States. After the revocation of his visa, Defense Department lawyers concluded that National Defense University was not required to fire Garcia Covarrubias because he had not been convicted of any crime, according to the article. With his Defense Department sponsorship, Garcia Covarrubias was allowed to work and travel in and out of the United States until his detention in Chile in November, 2013, according to the article. The article also reported that he continued to receive a salary from National Defense University until the end of his final teaching contract in February 2014, three months after the judge ordered him to stay in Chile.

The Pentagon issued a statement to McClatchy declaring that it had “developed formal guidance that specifically states all future foreign hires will undergo ongoing human rights vetting for the duration of their employment,” according to the article. Pentagon spokesman Joe Sowers did not return calls for comment from the Center for Public Integrity.

A senior U.S. government official said that after looking closely at Garcia Covarrubias’ record in recent days, we “found many links to torture allegations, from multiple open sources” as well as from nonpublic sources, which government experts considered credible. The official expressed frustration about Garcia Covarrubias’ hiring by NDU, explaining that “it is not that difficult to do the kind of vetting that would have caught these cases. There is a secret system we set up….It’s called Google.”

Garcia Covarrubias did not reply to questions emailed by the Center for Public Integrity to his published address. But his lawyers in Chile in 2013, José Luis López Blanco and José Alejandro Martínez Ríos, said in a court document that “in his military career, our client distinguished himself from his beginnings in the Military School until his promotion to the rank of Brigadier, and his later retirement from the Army as a very distinguished official.” Despite the fact that the investigation into “possible crimes committed at the Tucapel Regiment” had gone on for years, they added, “there has not been any evidence that permits Brigadier Garcia to be charged as the perpetrator responsible for any crime.” Lopez Blanco did not respond to questions emailed to the address listed on his website.

Garcia Covarrubias and Ospina Ovalle are both graduates of the U.S. military’s School of the Americas, a U.S. Army school for Latin American military personnel that closed in 2000 following years of criticism that it had advocated torture in training materials and graduated some of the region’s most notorious dictators, including Manuel Noriega of Panama and Leopoldo Galtieri of Argentina.

As a teenage cadet in the mid-1960s, Ospina Ovalle attended an orientation course at the School, according to a database compiled by School of the Americas Watch, an advocacy group. The organization seeks to permanently close the school, which reopened in 2001 under a new name: the Western Hemisphere Institute for Security Cooperation, based at Ft. Benning, Georgia.

Garcia Covarrubias took the School’s course “Combat Arms Orientation O-37” in 1970, according to the School of the Americas Watch database.

NDU has close ties to the Institute: A former director of the Perry Center in the last decade was one of the founders of the Institute, and a former deputy director of the Perry Center was an executive liaison there before joining the Center’s administration. Delegations from the schools routinely visit one another, and honor each other with awards such as the “Dr. William J. Perry Award for Excellence in Security and Defense Education.”

Sen. Leahy’s amendment to the Foreign Assistance Act, introduced in 1997 and enacted into law in 2008, requires recipients of State Department assistance or Defense Department-funded training programs for foreign security forces to be vetted through an internal State Department database, and bars assistance to individuals credibly charged with “a gross violation of human rights.”

Several government officials said that NDU officials had not interpreted the law as applying to candidates for teaching jobs and as a result did not submit the candidates to the State Department for appropriate review. That policy, they said, is presently under Pentagon review.