Like any military organization, the factions in the Cosmic Era depend on multiple ships to fulfill a wide variety of tasks. Listed below are the ship classes, the known ships of that class, and a simple explanation of the role in the battlefield. Individual ships do not have pages; their information can be found on their classes respective pages.
- Agamemnon-class carrier - Fleet flagships, carry at least 12 mobile weapons; Menelaos, Ortygia, Doolittle, Oda Nobunaga
- Archangel-class assault ship - Advanced transatmospheric warships derived from Orb's Izumo-class battleships, very well-armed and have high mobile suit capacity; Archangel, Dominion
- Arkansas-class cruiser - seaborne escort ship
- Hannibal-class land battleship - heavy land battleship; Bonaparte
- Des Moines-class cruiser - seaborne escort ship
- Drake-class escort ship - 130 meter escort ship; Bernard, Law, Seleukos, Antigonos, Belgrano, Xerxes
- Fraser-class destroyer - seaborne escort ship
- FX-550 Skygrasper - Support fighter capable of carrying and using Strike's weapon packs. Skygrasper unit #2 was an unlucky craft; in its brief life it was shot down twice and repaired both times before finally being destroyed.
- Girty Lue - Earth Alliance Special Forces ship, equipped with the Mirage Colloid, in violation of the Junius Treaty; two ship, the Girty Lue, answers to the leader of Blue Cosmos, Lord Djibril, and the Nana Balk, attacked the DSSD station to compel the AI unit of the Stargazer Gundam, was sunk by the propulsion laser from the Apollon A satellite.
- Nelson-class battleship - 250 meter battleship; Montgomery, Cassandros, Paris, Ptolemaios
- Spengler-class carrier - seaborne flagship and mobile suit carrier; John Paul Jones, Powell
- Compton class land battleship - Heavily armed ZAFT land battleship used during the Second Alliance-PLANT War; Compton, Uhlenbeck
- Eternal - Freedom and Justice support ship; carries the two METEOR prototype units; only one ship, Eternal
- Gondwana-class supercarrier - gigantic vessel with a huge mobile suit capacity; only one ship, the Gondwana. The Gondwana-class Supercarrier is a massive trans-atmospheric warship used by ZAFT, dwarfing even the battleship Minerva. The 1200-meter-long Gondwana is the largest space vessel ever built in C.E Universe. The Gondwana's massive size allows it to carry hundreds of mobile suits, and mounts a total of 16 linear catapults for launching them. The Gondwana is capable of operating on Earth and in space, despite its massive size. However, Gondwana primarily serves in outer space.
- Laurasia-class frigate - mobile suit carrying frigate (FFM); Gamow
- Lesseps-class land battleship - a large mobile ground base, it moves quite fast using a snakelike "scale system"
- Minerva-class battleship - Trans-atmospheric Mobile Suit Assault Ship (LHM), built to operate Second Stage MS Gundam units; derived from both Eternal and Archangel but of entirely new design; equipped with 2 standard linear catapults and a third dedicated catapult for the Impulse Gundam and its Silhouette packs; hangar capacity unspecified, but probably at least 10 mobile suits; LHM-BB01 Minerva
- METEOR - Mobile suit weapons support system (Mobile suit Embedded Tactical EnfOrceR), prototype; extends a Freedom/Justice-class mobile suit into a mobile armor, similar in concept to Gundam 0083's RX-78GP03D Gundam Dendrobium mobile armor
- Nazca-class destroyer - high-speed mobile suit carrying destroyer (DDMH), commonly used as fleet flagship; at least one unit was modified to use an anti-nuclear weapon known as the Neutron Stampeder; Vesalius,Voltaire,Holst
- Petrie-class land cruiser - Smaller land ships that serve primarily as escorts for *Lesseps-class vessels; Petrie, Henry Carter
- Vosgulov-class submarine - Large mobile suit-carrying submarines; Tsuigara, Vosgulov, St. Helens,Neila Bongo
- Messiah-Mobile Space Fortress - the Messiah base is heavily armed mobile space fortress and defended. Its most powerful weapon is Neo-GENESIS, a smaller variant of the massive GENESIS superweapon used in the First Alliance-PLANT War.
- Aegis-class cruiser - naval cruiser
- Heli - patrol/combat helicopter
- Izumo-class battleship - a modular ship prototype for the Archangel class; Kusanagi, Izumo, Kusano, Tsukumiya
- Kuraomikami-class destroyer - a naval warship
- Takemikazuchi-class carrier - flagship, built after the First Alliance-PLANT War; Takemikazuchi
- HOME (Junk Guild) - A modified cargo ship, used as a salvage vessel
- Lesseps - Salvaged and refitted ZAFT warship
- ReHOME (Junk Guild) - Also a modified cargo ship, replaces the HOME
- Silverwind - civilian space shuttle
- Tsiolkovsky (Civilian) - Designed and piloted by George Glenn to explore deep space