Mass Effect & Mass Effect 2
Due to the quarians' precarious existence and the need to enforce strict rationing, government is somewhat autocratic. The Migrant Fleet's operations are directed by the Admiralty, a board of five military officers who are advised by a legislative body called the Conclave.
Each vessel in the Fleet has the right to send representatives to the Conclave aboard the flagship. The number of representatives is based on crew size. Larger clans, with bigger ships and more votes, from the cores of political blocs. Opposition comes from the Outrider's Coalition, with delegates from thousands of smaller ships.
The Admiralty defers to the Conclave's decisions in most circumstances. However, if all five members agree that a Conclave decision jeopardizes the survival of the Fleet, and cannot get the Conclave to address their concerns, they have the right to summarily overturn the legislative decision. After the Admiralty uses extraordinary power, they must resign. If the Admiralty does not step down after using their veto, the rest of the military is obligated to arrest them.
Each ship captain has authority over his vessel, but is advised by an elected civilian Council, just as the Admiralty is advised by the Conclave. The relationship may range from cooperation to polite tolerance to outright hostility, but any captain who overrules his Council without good reason is relieved of commend by the Admiralty.
Many quarian ships are owned by clans who pool their resources to purchase used vessels from private sellers. Large ships are prestigious for big, rich clans, but a small ship means status for a small clan with enough personal wealth to afford a private vessel. Clan vessel captains are not subject to dismissal by the Admiralty; abusive captains are a 'family' problem if they do not disrupt the operations of the fleet.