Interior Minister Miguel Angel Osorio Chong told reporters at least 80 people were injured in the blast, CNN reported.
"People were screaming. ... You could see pieces of the wall falling to the ground," said Joaquin Borrell Valenzuela, an attorney for the Pemex comptroller's office.
A large plume of smoke was seen near the office tower, where dozens of people were trapped inside, Foro TV said.
Some of the injured were removed from the scene in stretchers, while helicopters airlifted others to local hospitals.
Pemex spokesman Francisco Montano told Notimex the explosion occurred in the basement.
The cause of the blast was unknown.