Trouble means covering for government department (9)
I believe the answer is:
incommode
'trouble' is the definition.
(both can mean inconvenience)
'means covering for government department' is the wordplay.
'means' becomes 'income' (someone's financial means).
'covering for' means one lot of letters goes inside another.
'government department' becomes 'mod' (Ministry of Defence).
'income' placed around 'mod' is 'INCOMMODE'.
(Other definitions for incommode that I've seen before include "Bother" , "Hassle" , "inconvenience" , "Trouble" , "Put out" .)