Generally speaking,
Star Trek has been quite vague about how Starfleet's higher echelons are organised. Starfleet appears to be administered and directed by Starfleet Command (also called "Fleet Headquarters" and "the Admiralty"); Starfleet Headquarters is a large building located in "San Francisco's old city peninsula". Although the President of the United Federation clearly has supreme command of Starfleet (most notably shown in
The Undiscovered Country and "Paradise Lost"), he is the only clear example of civilian control, not counting the Federation Council; the Federation Council, which also appears to have supreme command, actually has four uniformed, commissioned officers of Starfleet seated within it in
The Voyage Home (two Andorians and two Caitians).
The principal uniformed officer of Starfleet is the Commanding Admiral (ADM Heihachiro Nogura as of
The Motion Picture); oddly, the Commanding Admiral has some undefined relationship with various groups within the United Federation (VADM Lori Ciana, a zenopsychologist on ADM Nogura's staff, was "in charge of Starfleet Command's relationships with non-human species" and "Nogura's personal representative to the
new human groups here at home"). The films have used other titles for this office; ADM Harry Morrow is "Commander, Starfleet" in
The Search for Spock (the official site calls him "Starfleet's Chief of Command") and ADM William Smillie was "C in C" in
The Undiscovered Country. Mr. Roddenberry's
The Motion Picture novelisation indicates that the Commanding Admiral is assisted by not less than two staffs, the Commanding Admiral's Staff (a general staff presumably responsible for Starfleet's defence functions) and the Science Staff (presumably responsible for Starfleet's exploratory functions).
There have been only a bare handful of glimpses of other senior positions within Starfleet. ADM Robert Bennett is Chief of Staff in
The Final Frontier (presumably the Chief of the Commanding Admiral's Staff), while VADM James Tiberius Kirck is Chief of Starfleet Operations in
The Motion Picture (which the novelisation specifies to be an office of the Commanding Admiral's Staff responsible for fleet deployment) and evidently superintendent of Starfleet Academy in
The Wrath of Khan. VADM Thomas Henry is Chief of Starfleet Security in "The Drumhead" (ADM Ranar appears to have replaced him as Chief of Starfleet Security in "The Pegasus"), VADM Fujisaki appears to be Deputy Chief of Starfleet Intelligence in "Inter Arma Enim Silent Leges", RADM Bennett is Judge Advocate General in "Doctor Bashir, I Presume?", and ADM Brand was Superintendent of Starfleet Academy in "Journey's End" (she appears to have been subsequently replaced by a male Bolian in "Paradise Lost"). It is not clear where exactly Deputy Director Luther Sloan figures into the upper levels of Starfleet Command.
Flag officers are more often seen commanding Starbases and spaceborne facilities (ADM Budrow commands Starbase TWENTY-NINE in "Frame of Mind", RADM Chekote commands Starbase TWO-TWENTY-SEVEN in "Gambit, Part I", ADM Cobum commands Starbase TWO-THIRTY-FIVE in "Favor the Bold", ADM Drazman commands the Proxima Maintenance Yards in "Past Tense, Part I", ADM Haden commands Lya III Command Base in "The Wounded", ADM Marcus Holt commands Deep Space THREE in "Interface", VADM Nakamura commands Starbase ONE-SEVENTY-THREE in "The Measure of a Man" and as an ADM commands Starbase TWO-NINETEEN in "Phantasms", ADM Mitchell commands Starbase NINETY-SEVEN in "Starship Mine", ADM Uttan Narsu commands Starbase TWELVE in "Power Play", ADM Patterson appears to command the Utopia Planitia Shipyards in "Relativity"). Presumably, these officers have areas of responsibility (AOR) around their respective commands (otherwise it would make little sense for flag officers to be placed in command of space stations).
Other flag officers are placed in command of task forces, groups, and elements (ADM Gilhouly commands a task force deployed to Deep Space NINE in "By Inferno's Light", ADM J. P. Hanson commands Starfleet's battle force at Wolf 359 in "The Best of Both Worlds", ADM Hastur commands the task element deployed to Deep Space NINE in "The Way of the Warrior, Part II", VADM Hayes commands the battle force which intercepted the Borg in the Typhon Expanse in
First Contact). There are numbered fleets (e.g., the Second, Fifth, and Ninth Fleets mentioned in "Favor the Bold"), but most ships appear to operate more or less independently (perhaps organised into administrative squadrons and groups?).
COMs in
Star Trek, as in real life, tend to straddle the line between CAPTs and the various flavours of ADMs; COM Matthew Decker commands USS
Constellation (NCC-1017) in "The Doomsday Machine", while COM Domínguez commands Corinth IV Starship Base in "The Man Trap" and COM José I. Méndez commands Starbase ELEVEN in "The Menagerie, Part I". There have been a handful of occasions, such as "Reunification", where a CAPT has been shown to command a squadron (and therefore by tradition would be a "courtesy commodore"), but these have always been
ad hoc groupings.
The technical manual referred to by Darth_Zod was Mr. Joseph's
Star Fleet Technical Manual, which included a handful of organisation charts (rearranged in text format):
Star Fleet Armed Forces
Federation Council (Article 52, Section 2)
-Military Staff Committee (Article 52, Section 2)
--Star Fleet Command (Chapter VIII)
----Advisories
----Representatives
---Fleet Operations
---Base Operations
---Logistics Support
---Personnel Division
---Security Division
---Science Division
---Engineering Division
---Medical Division
---Technology Support
---Colonial Operations
---Justice Division (Supreme Court Statute, Chapter II, Article 15, Section 2)
---Galaxy Exploration
---Space Safety Board (Interplanetary Commerce Statute, Part VIII, Section 47, Item 01)
---General Accounting
---Star Fleet Academy
---Planetary Relations
Director, Military Staff Committee
----Deputy Director
----Chief Counsel
--Representative, United Federation of Planets
--Chief of Staff, United Nations of Earth-Sol System
--Chief of Staff, Planetary Confederation of 40 Eridani
--Chief of Staff, United Planets of 61 Cygni
--Chief of Staff, Star Empire of Epsilon Indii
--Chief of Staff, Alpha Centauri Concordium of Planets
--Chiefs of Staff, Other Invitational UFP Member Planets
--Representatives, Other Invitational UFP Social Systems
Chief of Staff, Star Fleet Command
----Deputy Chief of Staff
----Staff Adjutant
--Chief of Operations
--Chief Tactician
--Chief of Logistics
--Chief of Personnel
--Inspector General
--Chief of Engineering
--Chief of Technology
--Judge Advocate General
--Comptroller General
--Surgeon General
--Chief of Planetary Relations
--Navigator General
--Chief Cosmologist
--Chief of Sciences
--Chief of Astronautics
--Chief of Exploration
--Chief Alienologist
Chief of Operations
----Vice Chief of Operations
----Asst. Vice Chief
--Deputy Chief, Fleet Operations
---Asst. Deputy Chief
---Staff Adjutant
---Chief, Planetary Auxiliary Forces
---Chief, Fleet Operations Readiness
---Chief, Planning and Policy
---Chief, Requirements Analysis
---Chief, Fleet Reserve Forces
---Chief, Fleet Strategic Forces
---Chief, Fleet Tactical Forces
---Chief, Fleet Scouting Forces
---The Operating Forces of Star Fleet
--Deputy Chief, Base Operations
----Asst. Deputy Chief
----Staff Adjutant
---Chief, Maintenance and Repairs
---Chief, Facilities Staff Personnel
---Chief, Requirements and Plans
---Chief, Furnishings and Logistics
---Chief, Planetary Facilities
---Chief, Star Fleet Headquarters
---Chief, Star Base Facilities
---Chief, Fleet Maintenance and Repair
---The Star Fleet Supportive Facilities
Chief of Logistics
----Vice Chief of Logistics
----Asst. Vice Chief
--Chief, Planetary Sources
--Chief, Inventory Accounts
--Chief, Fleet Operating Supplies
--Chief, Star Base Supplies
--Chief, Recoverable Resources
--Chief, Storage Facilities
--Chief, Special Services
--Chief, Transportation Management
--Chief, Requirements Analysis
--Chief, Colonial Supplies
--Chief, Transport Personnel
--Chief, Transport Maintenance
--The Transport Forces of Star Fleet
The Inspector General
----Vice Chief of Security
----Asst. Vice Chief
--Chief, Fleet Security Forces
--Chief, SFHQ Security Force
--Chief, Base Security Forces
--Chief, UFP Court Officers
--Chief, UFP Penal Forces
--Chief, Planetary Marshalls [sic]
--Chief, Requirements Analysis
--Chief, Internal Investigation
--Chief, Weaponry Management
--Chief, Colonial Security
--Chief, Planning and Policy
--The Security Forces of Star Fleet
The Star Fleet Academy (Article 52, Section 4)
Commandant
----Deputy Commandant
----The Board of Regents
--Vice Commandant, The Cadet School
--------Asst. Commandant
--------Staff Adjutant
---Chief, Admissions and Placements
---Chief, Cadet Welfare Administration
---Chief, Corps of Cadets Officer's Council
---Chief, Cadet Basic Training
---Chief, Physical Fitness and Recreation
---Chief, School of Basic Studies
---Chief, School of Technical Studies
---Chief, School of Liberal Arts
---Chief, School of Special Training
---Chief, School of Military Arts
---Chief, Starship Flight Training
-----Academy Training Starships
---Chief Undergraduate Electives
--Vice Commandant, The Graduate Colleges
--------Asst. Commandant
--------Staff Adjutant
---Chief, Command Staff College
---Chief, College of Communications
---Chief, College of Engineering
---Chief, College of Law
---Chief, College of Medicine
---Chief, College of Navigation
---Chief, College of Science
---Chief, College of Technology
is that also durring ST III I could swear that I saw SF uniforms on some of the council members when they were deciding on what to do with Kirk.
