The most common and most likely answer to this crossword clue is the 4 letter word BRIG
I've seen this crossword clue in Financial Times
B
R
I
G
More clues leading to the result BRIG
- Officer briefly seen in naval prison
- Naval prison has transport to release indefinite number
- Queen boards large sailing ship
- British soldier back in prison
- Britain has rejected private sort of prison
- Army officer cut down, causing stir in navy
- Run aboard huge vessel
- King aboard great ship
- Sailor’s last in large ship
- End of spinnaker in large sailing ship
Buddy explains!

The straight part
We know that "ship" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case ship = brig.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does BRIG mean?
BRIG noun- A two-masted vessel, square-rigged on both foremast and mainmast
- A jail or guardhouse, especially in a naval military prison or jail on a ship, navy base, or (in fiction) spacecraft.
- Bridge.
- Brigadier.