The Galactic Federation classifies spacecrafts into several categories. Most of these can only be witnessed flying by or docked at various locations, but throughout the series Samus gets to visit quite a few vessels of different designs. Most notable of these is naturally Samus's very own Hunter-class Gunship.
- Main article: G.F.S. Tyr
Anhur-class warships are state-of-the-art Federation vessels, designed to police and defend planetary systems. One such ship, the G.F.S. Tyr was forced to land on Aether after engaging a Space Pirate convoy, just prior to the events of Metroid Prime 2: Echoes. During her visit on Aether Samus gets the rare opportunity to visit an Anhur-class ship.
Aries-class transporters are used to drop off marines to combat zones.
Griffin-class frigates are used as escort vessels to larger ships. The G.F.S. Theseus, which crashed on Bryyo, as well as G.F.S. Enkidu, which was docked at the Federation outpost on the planet Norion, were frigates of this class.
- Main article: Samus Aran's Gunship
Hunter-class ships are small, agile and armed to the teeth with firepower. They act as movable bases for one-man operations. Ideal for bounty hunters, all Samus's ships are Hunter-class. Samus's gunships contain mobile energy recharge systems and microfactories designed to produce ammunition. A sophisticated onboard computer stores mission data collected in the field for further reference.
Throughout the series Samus uses different models of the gunship, some of which are her own design. The gunship that appears in Metroid Prime 3: Corruption is equipped with a powerful Chozo biotech computer that can interface with Samus's command visor to deliver aerial bombardment to locations of her choosing. The ship also carries a biohazard scanner. All Samus's gunships utilize both Federation and Chozo technology.
Even though all of Samus's gunships are Hunter-class vessels, the category does not cover all types of small, private gunships. For example, the gunship used by bounty hunter Rundas is Phrygisian-class.
- Main article: G.F.S. Olympus
The Olympus-class battleships are the first Federation capital ships designed to use an onboard Aurora Unit. They are the flagships of the fleet they serve in, usually commanded by an officer of flag rank. Battleships of this class have smaller crews than most ships of a similar size due to the presence of the Aurora Unit. The space saved in crew support is used for more battle systems. The enormous vessels are powered by Fuel Gel, making the scarce commodity of extreme value to the Federation military. The G.F.S. Olympus and G.F.S. Valhalla were ships of this class.
The private gunship of bounty hunter Rundas was a vessel of this class. His ship is only seen in one location, but has two available scans, one before Samus battles Rundas and one after Rundas's death.
The Shrike-Class Assault Skiffs are rapid moving, unarmed skiffs produced by the Space Pirates using stolen Federation plans. The Pirates use them to transport their troops into battle. Samus first sees the Shrike in Agon then later in Torvus where the Pirate ambushed her in the Temple. 
- "The Anhur class is a state-of-the-art warship, designed to police and defend planetary systems. This ship, the G.F.S. Tyr, has been heavily damaged. It appears that the crew have dismantled parts of the Tyr as well, possibly for use as makeshift defense systems." —G.F.S. Tyr (Metroid Prime 2:Echoes)
- Scans made on G.F.S. Olympus in Metroid Prime 3: Corruption
- Metroid Prime 2: Echoes logbook: Samus's Gunship
- Metroid Prime 3: Corruption logbook: Hunter-Class Gunship
- Metroid Prime 3: Corruption logbook: Galactic Federation Data: Olympus-Class Battleship.
- Metroid Prime 2: Shrike-Class Assault Skiff