Hassle as government department cuts pay (9)
I believe the answer is:
incommode
'hassle' is the definition.
(I've seen this before)
'government department cuts pay' is the wordplay.
'government department' becomes 'mod' (Ministry of Defence).
'cuts' means one lot of letters goes inside another (some letters cut their way into other letters).
'pay' becomes 'income' (I've seen this before).
'mod' put into 'income' is 'INCOMMODE'.
'as' acts as a link.
(Other definitions for incommode that I've seen before include "Put out" , "Bother" , "Hassle" , "Trouble" , "inconvenience" .)