What does the cryptic crossword clue "Covert operator in unit measuring energy aboard old Spanish ship (5)" mean?

The definition is "ship". The wordplay uses a container (one word inside another). J (synonym="Joule, SI unit of energy") in NINA (synonym="NINA") = NINJA The answer is NINJA.

Covert operator in unit measuring energy aboard old Spanish ship (5)

Guardian Cryptic #29336 | 23 Down | 2024-03-21 flower

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