Streets surrounding the building were closed as evacuees wandered around, and rescue crews loaded the injured into ambulances.
"I profoundly lament the death of our fellow workers at Pemex. My condolences to their families," President Enrique Pena Nieto said via his Twitter account.
Shortly before the explosion, Operations Director Carlos Murrieta reported via Twitter that the company had reduced its accident rate in recent years. Most Pemex accidents have occurred at pipeline and refinery installations.
A fire at a pipeline metering center in northeast Mexico near the Texas border killed 30 workers in September, the largest-single toll in at least a decade for the company.
