After the final battle with Lucy, about 1/3 of real-world Japan's naval power ended up sunk. Also lost were many thousands of professional sailors and officers. Presumably, this compromised Japan's ability to defend itself during the Diclonius War.
Ships in the fleet included:
The Arii - flooded after encountering a 30m wave generated by Lucy.
The Imai - capsized along with the Arii after encountering the 30m wave.
The Hasegawa - flooded after encountering the 30m wave and was unable to steer towards the island.
The Fuyou - an escort vessel.
The Flagship was able to get Arakawa back onto the island and safely depart with the Anti-Diclonius Birth Vaccine, guided to it by the presence of hundreds of Clone Diclonii who sought to destroy it. Lucy's final acts of rage destroyed it. It is not Kirishima or Kongo as some fanfiction says.