Fleet Master is the highest version of Zealot except for Supreme Commander. Normally, they acts as the Ship Master, and controls only ship. But, when only a little part of a fleet needs to do an special mission or simply are needed elsewhere away from the rest of the fleet, a Fleet Master commands those few ships during that task.
Only one Fleet Master is officially known, and that's Voro 'Mantakree. He commanded a small task force to Onyx in order to follow the Covenant Destroyer Bloodied Spirit.