After the skirmish on Zebes, a special corps was assigned by the Galactic Federation to destroy the Metroids on SR388. That corps was never heard from again. The Supreme Council gave Samus the job to fly to SR388 and do what the special corps could not do--make the Metroids extinct.

Super Metroid manual

MSR Galactic Federation Council

The Galactic Federation Council is the governing body of the Galactic Federation. It is mentioned in the Metroid: Samus Returns introduction. It deemed the Metroids too dangerous to exist, and ordered Samus Aran to eradicate them on their homeworld of SR388. The council's apparent leader is a white skinned and haired human man in red, gold and white robes, who is seen delivering a rousing speech with a hologram of Metroids behind him.

In the Super Metroid manual, a Supreme Council is mentioned as a likely precursor, but not explicitly stated to be the Federation's ruling body. Neither game explains the membership of the council, but it is likely that some or most are human, as most of the members of the Federation seem to be in other Metroid games. It is possible, however, that individuals of other species may also be members. The council may be depicted in the Metroid Manga on Daiban with Chairman Keaton and Chairman Vogl.