Mexico has been hit by a wave of violence since launching the so-called "drug war," and activists and family members of the country's 40,000 missing persons have been denouncing mass graves for years.
But the report is the first time the authorities have done a nationwide survey to establish how many there are, and how many victims are buried in them.
It found 3,024 unmarked graves nationwide, with at least 4,974 bodies, Karla Quintana, head of the national search commission for missing persons, told a news conference alongside President Andres Manuel Lopez Obrador on International Day of the Disappeared.
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"This is the first time the federal government has recognized the number of unmarked graves," she said.
"This is not about numbers, though. These are people who are missing and whose loved ones are searching for them."
Authorities believe most of the victims were murdered by criminal gangs, sometimes in collusion with corrupt local officials, said Alejandro Encinas, deputy minister for human rights.
Families of the missing meanwhile protested outside the presidential palace, where the news conference was held, calling on the government to do more to find their relatives.
Carrying large pictures of their missing family members, they chanted: "Where are our children?"
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"The authorities ignore us. We the families are the ones who search, the ones who investigate, but when we bring them our information, they do nothing," said protester Maria Melo, whose brother
Matusalen disappeared in 2009 in the northern state of Coahuila, on the United States border.
Lopez Obrador, an anti-establishment leftist, has vowed to stop the spiral of violence and do more to find the missing, including by stepping up efforts to identify the 26,000 unidentified bodies in the country's overflowing morgues.
However, violent crime rates have so far increased under his administration.
Experts say Mexico's militarized anti-narcotics strategy has had the unintended effect of breaking the country's powerful cartels into smaller, more aggressive groups that then wage bloody turf wars, often with gruesome levels of violence.
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