Federation Commander

[lightsenshi]

At least not in the sense that many people seem to think. Why? Okay, let's do some backtracking....to the original series.

First off: Starfleet is depicted and operates as a military (specially naval) organization.
Secondly: Of the various major races, the two depicted as the largest and/or closest (Klingon and Romulan) are shown to be militant and expansionist. The Gorn aren't given more than a passing look and the Tholians are more interested in capturing the Enterprise than destroying her (which could clearly be construed either way).

As such: The idea that the Federation would refuse to have "warships" really doesn't fit the environment. Such ships would certainly exist, but would probably operate mostly in the central areas, either as a defense and/or reactionary force.

[Nerroth]

If you are referring to how the Federation has been portrayed in the post-1979 on-screen Franchise, that is one thing. But here in the Star Fleet Universe, Star Fleet itself is explicitly referred to as a "navy".

As noted in Prime Directive Federation (which is available in various game systems, such as GURPS 4th Edition), the SFU has a number of uniformed services operating within the United Federation of Planets.

Star Fleet itself operates as the "space navy", with a series of numbered fleets assigned to different areas of space. The Home Fleet protects the area surrounding the Federation capital zone (where Earth, Vulcan, and Andor can be found); the Third Fleet patrols the Klingon border; the Sixth Fleet watches the Romulan border; and so on and so forth.

Aside from Star Fleet, the Federation Police operates as a "space coast guard"; its police cutters can be found across Federation space, except in the Orion Enclave (where it is barred from operating).

Below the "federal" level, the major member planets each have heir own National Guards; remnants of the old "planetary" fleets they had operated prior to the formation of the unified Star Fleet. Each of the National Guards operates older ship compared to those in service with Star Fleet, albeit with their weapons upgraded to "modern" standards.

Other empires in the Alpha Octant have equivalent services, though how they function varies depending on the local politics involved. In Klingon space, the "space police" ships are operated by the Internal Security Force, but is tasked with missions that the Federation Police are not (such as providing the balance of forces required to win a civil war in he event that a portion of the Deep Space Fleet were to rebel against the Empire). In Romulan space, the local equivalent of the "national guard" ships are controlled by the various Great Houses, who are liable to set their own House's interests above those of the Empire at large.
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FC Omega Discussion (v3)
FC LMC Discussion

[Steve Cole]

In the Star Fleet Universe, the Federation is economically aggressive, using its great wealth to buy friends, ships, weapons, and get involved in foreign wars such as sending convoy loads of weapons and materials to the Kzintis. The Klingons are genuinely concerned that the Federation will eventually collect enough wealth in the Fed national treasury to just buy the Klingon Empire from the emperor and raise the standard of living (while sending 2/3 of the Klingon military into the unemployment lines).

In on-screen trek, it's kinda all over the map, a true navy here, a purely exploration force there, as each writer has his/her own take. (Some of the writers have no real idea what a military force is or does.) In one series they (mis)used the term "military" to refer only to things like Marines, commandoes, and ground troops. But Star Fleet has weapons, military ranks, command structures, and politics ultimate comes out the barrel of a gun.
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The Guy Who Designed Fed Commander

[Magnum357]

Also keep in mind that the TOS series says that only 12(13) of the constitution class where built. However, we know that the basic hull concept was still produced after the class retired. For example, CCH hulls where produced numerously after the CA+ retired.

To give another opinon on your question of Military versus scientific duties of the Starleet. GSC where produced in somewhat large quantities (maybe that is what the Constitution class really is) for exploration/diplomatic duties.