The agency had earlier reported eight dead and nine injured.
A crane on the Pemex tanker ship Quetzalcoatl was being repaired in the Gulf port of Coatzacoalcos, in the Pajaritos petrochemical complex, when the explosion occurred around noon, the company said.
The two missing people were "apparently close to the location of the blast," the Pemex statement read.
The company said the tanker had been emptied of fuel and was out of commission for maintenance.

Copyright AFP (Agence France-Presse), 2006