Government department has uncertainty with unknown change (6)
I believe the answer is:
modify
'change' is the definition.
(modifying is a kind of changing)
'government department has uncertainty with unknown' is the wordplay.
'government department' becomes 'mod' (Ministry of Defence).
'has' says to put letters next to each other.
'uncertainty' becomes 'if' (I've seen this in other clues).
'with' means one lot of letters go next to another.
'unknown' becomes 'y' (algebra).
'mod'+'if'+'y'='MODIFY'
(Other definitions for modify that I've seen before include "Adjust" , "Make partial changes to" , "temper" , "Partially change" , "Adapt" .)