Trouble getting revenue, defence ministry admitted (9)
I believe the answer is:
incommode
'trouble' is the definition.
('incommode' can be a synonym of 'trouble')
'revenue defence ministry admitted' is the wordplay.
'revenue' becomes 'income' (I've seen this before).
'defence ministry' becomes 'mod' (I've seen this in other clues).
'admitted' indicates putting letters inside.
'income' enclosing 'mod' is 'INCOMMODE'.
'getting' is the link.
(Other definitions for incommode that I've seen before include "Trouble" , "inconvenience" , "Bother" , "Put out" , "Hassle" .)