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The blast, which media reports said was caused by machinery, hit the lower floors of the downtown building, throwing debris into the streets and sending workers running outside.
Interior Minister Miguel Angel Osorio Chong told Mexican television the blast had killed 14 people and injured 80. It was not yet clear what caused the explosion, and the death toll could still rise, he added.
Police quickly cordoned off the building, and television images showed the explosion blew out windows on the lower floors of the tower and damaged the ground floor. Some people at the scene said the blast came from a neighboring building.
"The place shook, we lost power and suddenly there was debris everywhere. Colleagues were helping us out of the building," witness Cristian Obele told Milenio news network.
Helicopters buzzed around the building and lines of fire trucks sped to the entrance, while emergency workers ferried injured people through wreckage strewn on the street.
Pemex said initially the building had been evacuated because of a problem with its electricity supply. It then said there had been an explosion, but did not say what caused it.
Plaster fell from the ceiling of the basement, and the situation at the Pemex tower was dangerous, a spokesman for local emergency services said.
Pemex has experienced a number of deadly accidents in recent years. In September, 30 people died after an explosion at a Pemex natural gas facility in northern Mexico.