Exploiting legal loopholes and inaction across several government agencies, the accused torturer was able to remain in the United States, renew his work contract twice and even travel widely despite his visa revocation, a McClatchy investigation reveals.

The Pentagon now promises changes to its vetting process for foreign nationals working throughout its National Defense University, with an emphasis on accusations of human rights violations.

Officials with the U.S. military school – the William J. Perry Center for Hemispheric Defense Studies – knew by at least 2008 that Jaime Garcia Covarrubias had been accused of being part of Chile’s brutal secret police and stood accused of torture and murder.

Yet after the State Department revoked his Defense Department-sponsored visa on June 18, 2011, and a special U.S. human rights violator unit notified defense officials afterward, Garcia Covarrubias was paid sick leave and collected an annual salary in excess of $100,000 until February 2014.

The compensation was paid despite recommendations from the U.S. Embassy in Chile that Garcia Covarrubias face deportation proceedings and potential removal from the United States because of the allegations.

The handling of the matter, some critics say, casts doubt on the U.S. commitment to human rights. Multiple government sources, who insisted on anonymity because of the sensitivity of the matter, confirmed that once the State Department revoked his visa, no one else moved aggressively against Garcia Covarrubias, partly in deference to the Defense Department.

Garcia Covarrubias was not called in for a hearing by Immigration and Customs Enforcement, which reached out to the Defense Department. Pentagon lawyers shrugged off the visa revocation and said the school had no grounds to fire Garcia Covarrubias, even renewing his contract to teach after he took advantage of immigration laws to remain in the country.

“This is extremely troubling. Someone has to be held accountable within the Obama administration and in the Defense Department,” said Jose Miguel Vivanco, director of the Americas division of Human Rights Watch, an advocacy group. “It’s really hard to believe that it was just a lack of oversight by the Pentagon.”

The allegations against Garcia Covarrubias, reported in detail by McClatchy on March 12, sparked disagreement between the U.S. military and the diplomatic corps over how to deal with the case.

U.S. immigration laws allow revocation of visas or expulsion from the United States over the accusation of being a human rights violator. The State Department usually makes this determination but the Department of Homeland Security has ultimate say.

In Garcia Covarrubias’ case, U.S. Embassy officials in Chile were struck by a compelling account from one of the alleged victims and early on recommended that the professor be subjected to deportation proceedings.

“It was a very troubling, poignant and compelling rendition,” said a former U.S. official with close knowledge of the case, having never discussed the accuser’s account before with the media. The former official demanded anonymity because the Garcia Covarrubias affair remains an open legal matter in Chile.

Despite the accusations, Defense Department lawyers repeatedly concluded that the school, part of the National Defense University, was not compelled to fire Garcia Covarrubias because he had not been convicted of a crime. And school officials thought highly of his teaching abilities and expertise in the transition from military to civilian rule in Latin America. Garcia Covarrubias was a military leader during Chile’s dictatorship and in subsequent elected governments.

“Termination of a faculty member for misconduct must be based on a determination that the allegations are substantiated, after the employee is provided due process,” said a written response from the Pentagon to McClatchy’s questions about the case, adding that “Dr. Garcia had not been found guilty in any case brought against him in the Chilean justice system.”

In a separate followup statement, the Pentagon noted human rights accusations sometimes occur decades after the fact, and an internal review underscored the need for a “stringent new process to scrutinize the background of new hires.” This would include input from human rights groups.

“To further support these checks, (the Pentagon) has developed formal guidance that specifically states all future foreign hires will undergo ongoing human rights vetting for the duration of their employment,” the statement said.

The burden of proof cited by the Defense Department for its inaction isn’t necessary for the State Department, because many countries have weak justice systems that allow violators to escape any real consequences for their actions.

In the Chilean professor’s case, former school officials said he was hit by the State Department with a “provisional revocation.” This type of action was ushered in following the 9/11 terror attacks and makes it easier for the government to quickly bar the holder of a revoked visa from re-entering the United States without a new visa.

So how did an accused murderer and torturer remain in the United States with a revoked visa and was even permitted to travel abroad?

Even though his visa was revoked, there were no deportation proceedings or even a notice to appear before an immigration judge. Garcia Covarrubias was actually entitled to remain in the United States until this revoked visa would have expired, on Jan. 30, 2012, current and former government officials confirmed.

Immigration and Customs Enforcement had little room to move. His visa was sponsored by the Defense Department, limiting the ability to pursue criminal or immigration fraud charges. Defense officials were put on notice about the revocation and chose not to terminate his contract, even renewing it later.

As a result, Garcia Covarrubias was able to apply on Nov. 14, 2011, for lawful permanent residency. He was granted what’s called “advance parole,” and he acquired related permission to work and to travel. Those actions trumped the visa revocation when, according to one former school official, Garcia Covarrubias returned to the United States on separate occasions from the Dominican Republic and Mexico and was screened and permitted back into the country by Customs and Border Protection supervisors.

The allegations against Garcia Covarrubias date back more than 12 years, according to his attorney. The legal wrangling moved in fits and starts over these years, with one judge shelving the case in 2010 and giving the professor a document that said there were no active charges against him.

But on Nov. 8, 2013, a new judge, Alvaro Mesa Latorre, ordered Garcia Covarrubias to stand trial for the murder of seven political prisoners in November 1973, weeks after a U.S.-backed coup toppled an elected socialist government and installed a military dictatorship led by Gen. Augusto Pinochet.

Under the Chilean legal system, an investigative judge has both powers of the grand jury and prosecutor. Bringing charges there means the judge feels there are grounds to presume guilt.

Recent court documents filed by the former professor’s lawyers in Chile proclaim Garcia Covarrubias’ innocence and note that he has cooperated with testimony to investigative judges at least 12 times.

In an email to McClatchy, Attorney Jose Lopez Blanco called the claims against his client “totally biased” and made by people “wishing to develop a very negative image of other institutions of the West.”

Even the charges, however, were not enough to have the center terminate the professor’s employment.

“The best evidence that the case is rock solid is not only the indictment coming from a local judge in Chile, but the judgment of the State Department itself,” said Vivanco, the rights advocate. “The protection from the Defense Department smells really bad.”

The author of existing U.S. laws to keep American aid out of the hands of human rights abusers is among those now demanding answers from the Pentagon.

“The Department of Defense should know better than to invite in and continue to employ a foreign military officer for a position of authority at a prestigious U.S. institution even after he was credibly implicated in serious crimes,” Sen. Patrick Leahy, D-Vt., told McClatchy. “We criticize other countries for failing to hold accountable officers who violate the law. Yet, in this case, we reward him in our own country? It sends a terrible message.”

Garcia Covarrubias’ final contract ended almost three years after his visa revocation, not as a result of the murder-torture allegations but rather because of his scant chance for swift return to the states.

“There was no way that Chile was going to resolve his case in time for him to make any attempt to return to the U.S.,” said Kenneth LaPlante, who was the Perry Center’s deputy director and was with Garcia Covarrubias when the Chilean was told of the visa revocation in June 2011 by the deputy chief of mission in the U.S. Embassy.

Garcia Covarrubias’ alleged role in the murders and torture had been known by the school since at least 2008 and was the subject of tense internal emails. Martin Edwin Andersen, then the center’s communication director, raised them with the school’s leaders and now claims in a complaint that he was retaliated against for raising the issue.

At the time, school officials told Andersen that the U.S. government had nothing on Garcia Covarrubias.

“I have been involved in situations involving unproven allegations before – and the potential of harming the reputation of a person who may be wrongfully accused is also a major consideration that weighs heavily with me,” Richard Downie, then the director of the school, wrote to Andersen in a Nov. 12, 2008, email.

He then ordered Andersen to back off.

“I remind you that you are our chief of strategic communications and were not hired to be an investigative journalist,” Downie added.

Andersen also asked about allegations that Garcia Covarrubias belonged to Chile’s maligned National Intelligence Directorate, known as DINA. His name was on a list of agents provided by the Chilean military to a judge in 2008.

The DINA was disbanded in 1977 by the dictatorship after a series of assassinations of regime opponents across the globe, including a car bombing in Washington that killed Orlando Letelier, Chile’s former foreign minister, and his American aide.

It fell to LaPlante, then the school’s deputy director, to look into the DINA allegations.

“I asked him were you ever a member of the DINA,” LaPlante said. “He said, ‘No, I was an instructor at the intelligence school.’ It was asked and answered.”

The Garcia Covarrubias affair also raises questions about why it did not appear in the annual human rights report published by the State Department. This report is done country by country and details allegations, old and new, that remain in the public eye.

McClatchy reviewed a decade of reports, which often mentioned cases involving prominent government officials and cases involving Americans or regime crimes committed abroad. The allegations against Garcia Covarrubias are similar to cases listed in past reports, but he does not appear. Internal policy, said a State Department official who wasn’t authorized to speak to the media and demanded anonymity, is to limit the number of examples to three or less , preferring illustrative examples over a large number of cases.

U.S. Embassy officials in Chile said they could not comment on Garcia Covarrubias’ case because of privacy laws.

“We fully support and adhere to laws that prevent human rights violators from traveling to the United States,” said a statement from the U.S. Embassy in Chile. “Federal law prevents us from discussing visa record specifics of particular visa cases.”