Pemex said in a statement that firefighters had controlled Tuesday's blaze at the Antonio Dovali Jaime refinery in the southern state of Oaxaca.
As Pemex processes less oil, the utilization rate of its six domestic refineries - the volume of crude processed divided by refinery capacity - could sink to as low as 63 percent this year.
Pemex said the man, a worker of the contracting firm Atzco, was given immediate medical attention but had no vital signs by the time he arrived at a hospital.
The company said in a statement that the plant at the Ciudad Madero refinery located in northern Tamaulipas state has been isolated to attend to the leak.
The Mexican oil giant said its plants were operating normally and that no-one was injured.
The Salamanca refinery is located in central Guanajuato state and is Pemex's fifth biggest plant.