What's the command structure at the top of Starfleet?

Question

We seem to meet an awful lot of mostly non-recurring admirals.

What's the command structure at the top of Starfleet?

Does Starfleet report to a Commander-in-Chief? Is the Federation Council involved? Is the President involved?

Answer 1

The Memory Alpha page on Starfleet has a section specifically on its organisation. It describes it as follows:

Direct commanding authority over Starfleet was a power of the Federation President. (DS9: "Paradise Lost", Star Trek VI: The Undiscovered Country) In addition, the Federation Council, the Federation's legislature, often directly influenced the service's operations and even issued orders on occasion. (TNG: "Force of Nature", "The Defector") The day-to-day operations of the service were managed by Starfleet Command, under a commander in chief. (Star Trek VI: The Undiscovered Country)

As for the command structure itself, we have several important figures:

• Commander in Chief

  The commander in chief oversaw the operations of the entire service, and reported directly to the Federation president. (Star Trek VI: The Undiscovered Country)

• Starfleet Command

  This was the service's operational authority. Senior positions included the Commander, Starfleet. the chief of staff and the chief of Starfleet Operations. (Star Trek III: The Search for Spock; Star Trek IV: The Voyage Home; Star Trek V: The Final Frontier)

• Sector Commands

  These oversaw operations of the service within sectors of Federation space. There were at least 23 sector commands. Sector commanders reported to Starfleet Command, and commanding officers of service vessels operating within these sectors reported to them. (TNG: "Power Play", "The Measure Of A Man")

In addition, there are a whole host of agencies within Starfleet. So, in answer to your questions:

1. Does Starfleet report to a Commander-in-Chief? Yes
2. Is the Federation Council involved? Yes: The Federation Council can order about Starfleet
3. Is the President involved? Yes, as outlined in the first quote, the President has full control over Starfleet

Answer 2

• In Star Trek VI, we see a man named Bill in Fleet Admiral's uniform introduced explicitly as The Commander in Chief. He is seen consulting with and taking orders from The Federation President in other scenes.
• In DS9: "Paradise Lost", The Federation President refers to himself as Starfleet Admiral Leyton's Commander-in-Chief.

The President is referred to as having been elected, suggesting a civilian position. We can interpret these facts in either of a couple of ways:

1. In the 79 years or so between Star Trek VI and Paradise Lost, the command and/or constitutional structure of The Federation and/or Starfleet changed. In 2293, Starfleet has a military CiC who reports to the civilian President; in 2372, Starfleet's CiC is The President of The Federation.
2. The top military official in Starfleet is referred to as the CiC, perhaps sometimes as Commander, Starfleet, and is subordinate to The Federation President. The President is CiC of Starfleet, as well as other Federation military and paramilitary entities, such as The Federation Naval Patrol.

The difference between the two scenarios appears academic: senior Starfleet personnel lead Starfleet, and answer to the civilian government, sometimes embodied by The President.

As for The Federation Council, it is generally depicted as a legislative body. Its edicts are imposed on Starfleet, but we have yet to see Councilors issuing orders to Starfleet personnel. The workings of Federation government have been left vague in canon, but an American-style separation of powers seems to be in effect.