But in all but a few cases, the allegations languish, are dismissed or are reclassified. “The impunity is a loud signal that crimes against humanity are being committed,” Mr. Goldston said.

The Justice Initiative report is the first time an international group has made a public legal argument that the pattern of abuses amounts to crimes against humanity. The finding is significant, Mr. Goldston said, because under the lens of international law, an investigation would seek to determine the chain of command behind the policy.

The government of President Enrique Peña Nieto rejected the conclusions.

“Based on international law, crimes against humanity are generalized or systematic attacks against a civilian population which are committed in accordance with a state policy,” the government said in a statement. “In Mexico the immense majority of violent crimes have been committed by criminal organizations.”

The report does not dispute that last point. Its analysis, which covers the six-year administration of former President Felipe Calderón and the first three years of Mr. Peña Nieto’s government, also looks at the Zetas, the most violent of Mexico’s drug gangs. Their brutal actions constitute crimes against humanity as well, the report concludes.

The government said that in the “exceptional cases” in which public officials have been shown to be involved in the use of excessive force, human rights abuses or torture, they have been tried and sentenced.

But human rights and international organizations have argued for years that these cases are not exceptional.