Under the program, 15 percent of the money for Mexico is allotted on the condition that the country improve the accountability of the federal and local police; ensure civilian investigations and, if warranted, prosecutions of allegations of abuse by the police and the military; and ban testimony obtained through torture or other mistreatment.

The State Department, in a report delivered to Congress on Friday, said it would release $36 million from earlier budgets. But it said it would withhold 15 percent of the $175 million allocated in the most recent budget.

“No society can enjoy domestic peace and security without a functioning justice system supported by appropriately trained and equipped law enforcement and justice personnel who are respectful of human rights and rule of law,” said a State Department spokesman, Harry Edwards.

The State Department called on the Mexican Congress to pass legislation strengthening the authority of the country's national human rights commission and subjecting military service members accused of human rights abuses to civilian prosecution.

The Mexican government, in a statement, called the findings an affront to its sovereignty. “The Merida Initiative is based on shared responsibility, mutual trust and respect for each country's jurisdiction,” the statement said.

Nik Steinberg, Mexico researcher for Human Rights Watch, said, “Any withholding of funds would be a step in the right direction, but given the total impunity for military abuses and widespread cases of torture, none of the funds tied to human rights should be released.”