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The 8.2 magnitude quake, one of the biggest recorded in the country, struck off the southern coast late on Thursday, causing cracks in buildings and triggering a small tsunami.
Alejandro Murat, the state governor, said 23 deaths were registered in Oxaca, 17 of those in Juchitan.
Seven people were also confirmed dead in the neighbouring state of Chiapas and two children were killed in Tabasco.
The quake, which the US Geological Survey said had a magnitude of 8.2, hit in the Pacific 102 miles west of Tapachula.
People still wearing pyjamas ran out of their homes and gathered in frightened groups.
Rodrigo Soberanes, who lives near San Cristobal de las Casas in Chiapas, the state nearest the epicentre, said his house “moved like chewing gum”.
The furious shaking created a second national emergency for Mexican agencies already bracing for Hurricane Katia on the other side of the country.
The system was expected to strike the Gulf coast in the state of Veracruz early on Saturday as a category two storm that could bring life-threatening floods.
The Pacific Tsunami Warning Centre said waves more than 3ft above the tide level were measured off Salina Cruz, Mexico. The warning centre said several Central American countries, including the Pacific coastlines of Guatemala, Honduras, Mexico, El Salvador and Costa Rica, were under threat.
The centre’s forecast said Ecuador, El Salvador and Guatemala could see waves of 3ft. No threat was posed to Hawaii and the western and South Pacific.
The earthquake struck at 11.50pm local time on Thursday, and was so strong it even sent panicked people into the streets more than 650 miles away in the country’s capital.
Buildings shook violently in Mexico City, where frightened residents gathered in the streets in the dark fearing buildings would collapse.
Luis Carlos Briceno, an architect, 31, who was visiting Mexico City, said: “I had never been anywhere where the earth moved so much. At first I laughed, but when the lights went out I didn’t know what to do.
“I nearly fell over.”
Hundreds of buildings collapsed or were damaged, power was cut to more than 1.8 million people and authorities closed schools in at least 11 states for safety checks.
Chiapas governor Manuel Velasco said three people were killed in San Cristobal, including two women who died when a house and a wall collapsed. He called on people living near the coast to leave their houses as a protective measure.
“There is damage to hospitals that have lost energy,” he said. “Homes, schools and hospitals have been damaged.”
Tabasco governor Arturo Nunez said two children died in his Gulf coast state. One of them was killed when a wall collapsed, and the other was a baby who died in a children’s hospital that lost electricity, cutting off the infant’s ventilator.
The US Geological Survey recorded at least 20 aftershocks of magnitude 4.0 or greater within about five hours, and the president warned that a major aftershock as large as magnitude 7.2 could occur.
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