Head of government in Scottish town backed complaint (6)
I believe the answer is:
niggle
'complaint' is the definition.
(a minor complaint or quibble)
'head of government in scottish town backed' is the wordplay.
'head of' indicates taking the first letters.
'in' is an insertion indicator.
'scottish town' becomes 'elgin' (town in Scotland).
'backed' is a reversal indicator.
The initial letter of 'government' is 'g'.
'g' placed into 'elgin' is 'elggin'.
'elggin' backwards is 'NIGGLE'.
(Other definitions for niggle that I've seen before include "Persistant annoyance" , "Trivial criticism or annoyance" , "A slight bother" , "Persistently irritate" , "Grumble" .)