Facility Command is a Space Pirate organization mentioned once in Metroid Prime. It would seem to oversee the successful operation of the Phazon Mines facilities. They are known for an order that Samus can read, demanding that two Elite Pirates be trained for battle.
Elite Control
"Facility Command's request for Elite Pirate transfer to security forces granted. Prepare units EPG-8644 and EPG-8656 for field duty at once."