The 17-page report was delivered to Congress last week as part of a joint counternarcotics program known as the Merida Initiative. The $1.4 billion initiative, passed by Congress last year, provides equipment and training to Mexican security forces. But it also calls for 15 percent of the money to be withheld until the State Department verifies that the government is meeting four human rights requirements, including the prosecution of police officers and soldiers responsible for abuses.

While the State Department cited several examples of progress, it was hardly a glowing endorsement. And a key Democratic senator said the report failed to adequately address the concerns about impunity within the Mexican military that led him to threaten to hold up millions of dollars in United States assistance.

“It is well known that the military justice system is manifestly ineffective,” said a statement issued Tuesday by Senator Patrick J. Leahy of Vermont, chairman of the Senate appropriations subcommittee on foreign operations, which must approve disbursement of the Merida assistance. “And it is apparent that neither the Mexican government nor the State Department has treated human rights abuses by the military, which is engaging in an internal police function it is ill suited for, as a priority.”

The report praised President Felipe Calderón’s “firm commitment” to ending a devastating wave of drug-related violence that has killed about 7,500 people in his country since the beginning of 2008. Mexico’s efforts, the report said, have been led by about 45,000 Mexican soldiers, deployed to support and, in some cases, replace beleaguered state and local law enforcement agencies across the country.

Since the beginning of 2007, the report states, Mexican security forces have seized about 65 tons of cocaine and more than 9.3 million pounds of marijuana. Arms seizures have soared to 9,500 weapons in 2007, from 4,220 in 2006, the report says. And the Mexican government has created a number of new mechanisms to make it easier for citizens to anonymously file complaints against rogue security officers.

But as the troops’ presence on the streets has increased, the State Department reported, so have the number of complaints against them. Between 2006 and 2008, they rose to 1,230, from 182, the report said. In all, Mexico’s National Human Rights Commission has received some 2,050 complaints against soldiers since Mr. Calderón took office at the end of 2006.

Based on those complaints, the human rights commission — which is financed by the Mexican government — issued 26 recommendations for follow-up to the Defense Ministry. The ministry agreed to consider 25 of them. And since soldiers accused of abuses are generally prosecuted in closed military tribunals, it was impossible to tell whether any complaints had resulted in punishments.

“The information received from the Mexican government regarding these cases,” the report said, “and the opaqueness of the military court system makes it difficult to analyze the nature and the type of complaints filed, the status of the cases against members of the military alleged to have violated human rights, or the results of the military prosecution.”

The State Department report says the head of a newly established military human rights directorate had announced that military courts had convicted 12 soldiers since 2006 and were investigating an additional 52 officers in connection with offenses including homicide, torture, kidnapping and extortion.

However, the State Department acknowledged that little was known about these cases.

Last week, at a summit meeting attended by President Obama, Mr. Calderón defended his government, saying allegations of human rights abuses were being aggressively investigated.

“In every case, there has been a scrupulous effort to protect human rights,” he said. “Anyone suggesting the contrary should prove a case, one single case, where the authority did not act.”

Human Rights Watch, which has been documenting abuses in Mexico, responded hours later with two cases, both from Mr. Calderón’s home state of Michoacán, in which soldiers accused of torture two years ago have not been prosecuted.

In an interview on Tuesday, Madeleine Penman, a spokeswoman for the Miguel Augustín Pro Juárez Human Rights Center, called on the United States to withhold the funds.

“There is very little evidence of action on human rights by the Mexican government,” she said. “We do not think that simply backing up Felipe Calderón’s fight against organized crime helps at all with rule of law in Mexico.”