Minister sees train regularly taken by nuisance (6)
I believe the answer is:
priest
'minister' is the definition.
(a church minister)
'train regularly taken by nuisance' is the wordplay.
'regularly' indicates alternate letters (regularly take one letter, leave next etc.).
'taken by' means one lot of letters goes inside another.
'nuisance' becomes 'pest' (I've seen this before).
The alternate letters of 'train' are 'ri'.
'ri' going into 'pest' is 'PRIEST'.
'sees' is the link.
(Other definitions for priest that I've seen before include "with orders" , "Man of the cloth" , "Spiritual leader" , "Religious teacher" , "person of religion" .)