Photos of missing students are presented during an march in Mexico City in support of 43 students from Guerrero state who were forcibly disappeared. (Edgard Garrido/Reuters)

In a setback for its multibillion-dollar effort to help Mexico fight its drug war, the U.S. State Department has decided that Mexico failed to reach some human rights goals, triggering a cutoff of millions of dollars in aid.

The move, which has not been reported previously, affects a small portion of the annual anti-drug funds given to Mexico. But it is a clear sign of U.S. frustration. It comes as Mexico has been roiled by several cases of alleged abuses by security forces, including the disappearance of 43 students in the southern state of Guerrero last year.

Through the Merida Initiative, a major U.S. program to support Mexico’s battle against its drug cartels, Congress has appropriated $2.3 billion since 2008 for equipment such as helicopters and border sensors as well as training programs for thousands of Mexican officials.

Fifteen percent of the money provided for the Mexican military and police is subject to provisions that the country make progress on protecting human rights, including enforcing rules against torture and prosecuting people for forced disappearances.

To release that money, the State Department is required to write to Congress showing how Mexico is taking steps to address those problems. But this year, officials chose not to write that report, and the 15 percent of the money for security forces, or $5 million, got diverted for coca eradication in Peru. The total Merida funding for the year was $148 million.

“It’s a big decision for them to have made,” said Maureen Meyer, a Mexico expert at the Washington Office on Latin America. “I think they basically decided we cannot honestly or in good faith say there’s been enough progress made in Mexico. It shows how concerned the U.S. is about the human rights situation in the country.”

As far back as 2010, the State Department and Congress have held up Merida money because of human rights concerns, but those funds eventually were provided after Mexico took action, such as passing human rights legislation and limiting the jurisdiction of military courts. This year, in contrast, Mexico lost the money.

“From time to time, countries are unable to meet the reporting criteria as required by Congress,” the State Department said in a statement in response to a question about the aid. “This year, we were unable to certify that Mexico fully meets the criteria.”

Over the years, U.S. diplomats have tended to cast the human rights record of Mexican security forces in the best possible light to keep them as willing partners in the war on drugs. The State Department decision to divert Merida funds to Peru was done without any public criticism of Mexico.

“They’ve handled this more with tweezers than with sledgehammers,” said Eric L. Olson, a Latin America expert at the Woodrow Wilson International Center for Scholars, in Washington. “But it undeniably sends a signal that the U.S. is not entirely pleased.”

The most recent State Department annual report on human rights, for 2014, noted that there have been numerous allegations that Mexican authorities “committed arbitrary or unlawful killings, often with impunity.” It also describes accusations of torture and disappearances by security forces.

Asked for comment on the cut in assistance, the Mexican Foreign Ministry said the U.S. certification of its human rights efforts — known as the “15 percent report” — is “an obligation imposed by the U.S. Congress on the government. It is not an obligation Mexico has to meet.”

Mexico’s policy is to observe the rule of law and to demonstrate “absolute respect for, and protection of, human rights,” the ministry said in its statement.

In recent years, as drug violence has soared and then declined somewhat, soldiers and police officers have regularly been accused of killing innocent civilians, torturing witnesses and using disproportionate amounts of force as they fight drug cartels. In several parts of the country, the Mexican military has taken over primary security duties after the municipal police were disbanded because they had been infiltrated by drug gangs.

“Despite years of the Merida Initiative and the efforts the United States has made to work with the Mexican government to improve justice and accountability, there has been little progress,” said Tim Rieser, a foreign policy aide to Sen. Patrick J. Leahy (D-Vt.). The “Leahy law” bars the U.S. government from providing aid to foreign military units that appear to have committed gross human rights violations.

A string of alleged killings

The most notorious recent case of alleged abuses by Mexican security forces involves the disappearance last year of 43 students from a teachers college. The Mexican government claimed that municipal police from the town of Iguala, in Guerrero state, turned the students over to drug traffickers who killed them and burned their bodies in a trash dump.

But investigators convened by the Inter-American Commission on Human Rights concluded last month that the students could not have all died in that fashion because such a large fire had not occurred. They also wrote that soldiers allegedly witnessed the violence but failed to intervene. Government investigators looking into the case mishandled evidence, and witnesses claim to have been tortured, the report said.

“Everyone knew that the spotlight was on this case,” Rieser said. “And yet even still, they tried to whitewash it and cover up what happened. It shows the amount of impunity that exists there and the belief that you can get away with anything.”

A few months before the students disappeared, the Mexican army allegedly killed 22 people, including shooting some execution-style after they had surrendered, in a warehouse in Tlatlaya, southwest of Mexico City. Human rights groups also have compiled allegations that witnesses to the killings were subsequently tortured. Three soldiers are facing homicide charges in the incident, and seven state police officers have been accused of torture.

In January, federal forces allegedly killed 16 civilians in Apatzingan, a town at the center of the militia uprising against drug cartels in Michoacan state.

Although these issues have raised concerns in Washington, the scandals do not appear to have generated much pressure to change broader U.S. funding to Mexico.

With Mexican President Enrique Peña Nieto facing intense domestic criticism and sinking approval ratings as he grapples with a limping economy and a difficult security situation, the Obama administration is careful not to pile on, said Carl Meacham, director of the Americas program at the Center for Strategic and International Studies. “They don’t want to exacerbate a situation that’s already incredibly sensitive.”

But given the string of alleged abuses, “it’s impossible to make the case anymore” that Mexico is progressing on human rights, said Stephanie Erin Brewer, coordinator of the international department at Centro Prodh, a human rights group in Mexico City. “This certainly is a very strong message for Mexico.”

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