There was no immediate cause given for the blast, which also damaged the first and second floors of the auxiliary building in a busy commercial and residential area.
But in a Tweet, Pemex said it had evacuated the building as a precautionary measure because of a problem with the electrical system.
The company later tweeted that experts were analyzing the explosion and any reports of a cause were speculation.
"It was an explosion, a shock, the lights went out and suddenly there was a lot of debris," employee Cristian Obele told Milenio television, adding that he had been injured in the leg. "Co-workers helped us get out of the building."
The tower, where several thousand people work, was evacuated.
