The most common and most likely answer to this crossword clue is the 3 letter word CID
I've seen this crossword clue in The Guardian
C
I
D
More clues leading to the result CID
Buddy explains!

The straight part
We know that "Department investigating" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case department investigating = cid.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.