The SS Shinobi was a Federation vessel in operation in the late 23rd century. In 2269 the vessel was under the command of Captain Gretel Gernsbeck.
While traveling in the Delphi sector in the 2260s, the Shinobi mysteriously disappeared. It was later revealed by the crew of the USS Enterprise that the omnipotent being known as Trelane, had captured the Shinobi, miniaturized her, and placed her inside a glass bottle.
In 2269, the Shinobi and other captured vessels were released and restored to normal thanks to the intervention of the Enterprise crew. (TOS video game: Judgment Rites)