Mexican government officials acknowledge the official Covid-19 death toll is a severe undercount.

Photo: Rebecca Blackwell/Associated Press

MEXICO CITY—Mexico’s true death toll from coronavirus is nearly double the government’s official count, according to a review of data from a Mexican government agency that suggests the country now has more than 50,000 coronavirus deaths.

Data from the country’s National Population Registry shows that between March 19 and June 19, some 38,815 people died from Covid-19, compared with an official tally from the country’s Health Ministry of around 20,394 on June 19. The data, obtained by the Mexican news website La Silla Rota, was reviewed by The Wall Street Journal.

Since June 19, Mexico’s official death toll has continued to grow. As of early Friday, it stood at 29,189. If the pattern found by the population agency between March 19 and June 19 continued to hold in the past two weeks—that Mexico is registering only roughly half the real death toll—that would suggest Mexico’s toll is fast nearing 60,000.

Mexico this week passed Spain in the number of deaths from the pandemic, and with about 600 or so deaths a day, will likely pass France this weekend, putting it only behind the U.S., Brazil, the U.K. and Italy.

Mexican government officials now acknowledge the official toll is a severe undercount, mostly because it only counts fatalities from people who tested positive for the disease and died in hospitals.

There are many reasons why that undercounts the true death toll. Mexico carries out the least testing of any major country, and only tests people who have severe symptoms at hospitals. Only 1 in 10 people with flulike symptoms who turn up at hospitals are even tested, according to government testing guidelines. Some hospitals report a shortage of testing kits and so don’t carry out any tests at all, even on their sickest patients. And an unknown number of Mexicans are simply dying at home.

Mexico’s coronavirus czar, Deputy Health Minister Hugo López-Gatell, said this week that the government was trying to assess the true number of deaths with help from the national statistics agency, the population agency, and the World Health Organization. He said the figures would be released shortly.

Separately, Mr. López-Gatell acknowledged that the country’s deaths had spiked to about three times the normal rate in recent months. He declined to give the number, saying it would be released in coming days.

“How many people have died now? This statistic, which we are still refining, is about three times more,” he was quoted as saying in The Washington Post.

Mexico carries out the least coronavirus testing of any major country. Here, a cemetery on the outskirts of Mexico City on Thursday.

Photo: Rebecca Blackwell/Associated Press

The government’s population registry estimate reviewed death certificates from across the country and counted cases where the cause of death was listed as Covid-19 or likely Covid-19. In Mexico City alone, it found 13,096 deaths listed as confirmed or likely Covid-19, compared with an official tally of 5,314.

In its count, the population registry didn’t include some 4,578 victims whose cause of death was listed as “atypical pneumonia”–a condition often associated with Covid-19 and influenza. Since the influenza period ended in Mexico in early April, many of those deaths could be due to Covid as well, analysts said.

A study published in a Mexican news magazine Nexos this week found that for Mexico City alone, excess deaths were 22,700 people from the end of March to late June compared with the same period from 2016-2019.

Mexico’s government spokesman Jesús Ramírez didn’t respond to calls seeking comment about the data.

Many countries are struggling to count the true number of people killed by the pandemic. In most nations, the easiest way to make that calculation is by looking at how many more people have died in recent months compared with a baseline of the same period in previous years.

In Spain, there was an excess mortality of 43,000 people from March to May, according to data from public registries, 59% higher than the official count of 27,000 deaths caused by the coronavirus.

But that calculation is harder in Mexico because the government doesn’t publish mortality data until the following year.

For months, there has been a debate in Mexico about the true toll, and calls for the government to make mortality data publicly available.

“Mexicans have a right to know the magnitude of the problem,” said Edna Jaime, head of a leading think tank in Mexico called Mexico Evaluates. “For example, there is too little testing in Mexico, and that generates a big undercount in cases and deaths, which in turn affects the information the government uses to manage the crisis.”

A paramedic checks a man with symptoms of Covid-19 in Ciudad Nezahualcoyotl, Mexico, on June 21.

Photo: pedro pardo/Agence France-Presse/Getty Images

Mexico carries out half the tests per capita compared with India, one 10th compared with Italy and one 20th compared with the U.S., according to Our World in Data, a nonprofit research project based at The University of Oxford. Mr. López-Gatell has said widespread testing won’t help the country cope with the pandemic, a position disputed by the World Health Organization.

In early May, several foreign media outlets, including The Wall Street Journal, the New York Times and Spain’s El País, published stories based on death certificate data and other projections that suggested the true death toll in Mexico was far higher than the official count.

For instance, in a sample of 105 death certificates in Mexico City, the Journal found that 52 had the cause of death listed as “possible” or “likely” Covid. But just four had confirmed Covid as the cause—meaning only those would qualify to enter the official count.

The administration of President Andrés Manuel López Obrador responded by sharply criticizing the media outlets, saying they “distorted reality.”

Write to David Luhnow at david.luhnow@wsj.com and Juan Montes at juan.montes@wsj.com

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