The Oaxaca state prosecutor's office said in a statement that five women, four men and three children were killed at the crash site and another person died later at the hospital.
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A state government official who was not authorized to be quoted by name said the chopper crashed into a group of people who had been spending the night outside after a powerful 7.2 magnitude earthquake hit the area. Aftershocks had caused people to flee their homes for fear they would collapse.
The Defense Department said the Blackhawk helicopter suffered the mishap when it was preparing to land on a vacant lot in the city of Jamiltepec, about 19 miles from the area of Pinotepa Nacional. The craft was carrying Interior Secretary Alfonso Navarrete and Oaxaca Gov. Alejandro Murat, neither of whom had serious injuries. The department said the victims had been waiting for the helicopter, but did not provide more details.
The accident was the latest embarrassment in little more than a month since Navarrete took over at the Interior Department, which oversees most political and security issues. Earlier this month, an intelligence agent from an agency overseen by Navarrete's department was caught tailing an opposition presidential candidate.
Both Navarrete and the defense department said they regretted the loss of life in Friday's accident.
The same city where the accident occurred also saw significant destruction from the earthquake. About 50 homes were damaged, as well as the town hall and church, according to the Interior Department.
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Two people suffered fractures and non-life threatening injuries in Pinotepa Nacional.
The damage was minimal compared to a massive 8.2 quake that struck in the same general area on Sept. 7 and a 7.1 magnitude quake on Sept. 19, which killed 471 people and damaged over 180,000 houses in eight states, including Mexico City.
But the magnitude 5.8 aftershock that struck Friday about an hour after the 7.2-magnitude quake led some residents of Jamiltepec to decide to spend the night outdoors, a common practice after strong shakes in the balmy region.
The military helicopter apparently flipped and fell on top of the townspeople as it attempted to land.
Navarrete told local media that "as the army helicopter we were travelling in tried to land, the pilot lost control, the helicopter fell and flipped."
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Jorge Morales, a local reporter who was aboard the helicopter when it crashed, described harrowing moments as the pilot lost control and the helicopter attempted to touch down in a swirl of dust.
"The moment the helicopter touched down it lost control, it slid-- like it skidded-- and it hit some vehicles that were parked alongside the area that had been defined for the landing," he told a Mexican television news program. "In that moment, you couldn't see anything, nothing else was heard beside the sound that iron makes when it scrapes the earth."
Navarrete and Murat were evaluating reports of damage from the earthquake before the helicopter crashed.
The U.S. Geological Survey originally put the magnitude of Friday's quake at 7.5 but later lowered it to 7.2. It said the epicenter was 33 miles (53 kilometers) northeast of Pinotepa in southern Oaxaca state and had a depth of 15 miles (24 kilometers).