The blast also injured at least 45 people and sent a cloud of noxious chemicals into the sky.
Local emergency officials said hundreds of people had been evacuated from the site in the Gulf state of Veracruz.
Television footage showed an initial burst of flames followed by a tower of thick smoke.
The cause of the blast is unclear, but Pemex warned local residents to keep their distance from the site due to what it described as a dissipating cloud of toxic fumes.
A company official said local oil exports were not affected.
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Hundreds of people have been evacuated following a blast at a Pemex oil facility in the southern port city of Coatzacoalcos in Mexico.
Three people have been reported injured.
The state-owned petroleum company said the blast will not have an impact on oil exports.
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