The blast occurred in the town of Kirishi on May 29. One person died in the fire following the blast, and four others were hospitalized with severe burns and other injuries. The explosion destroyed the compressor station and damaged other facilities at the refinery owned by oil company Surgutneftegaz.
"A 46-year-old man, who had 95% burns, has died," the source said.
The other three injured workers are currently in intensive care in a critical condition.
The blast is believed to have been caused by technical problems. The industrial safety regulator Rostekhnadzor and local prosecutors are investigating the cause.
The plant accounts for about 30% of Russia's low-sulfur fuel output, mainly for use in Russia's northwestern regions and for export to Western and Eastern Europe.
This is the second accident at the refinery this year. A fire in February, started by unauthorized welding, damaged an area of over 400 sq m, although there were no casualties.