Native American father is in pain (6)
I believe the answer is:
apache
'native american' is the definition.
(group of Native American tribes)
'father is in pain' is the wordplay.
'father' becomes 'pa' (pa can mean dad or father).
'is in' means one lot of letters goes inside another.
'pain' becomes 'ache' (ache is a kind of pain).
'pa' going within 'ache' is 'APACHE'.
(Other definitions for apache that I've seen before include "nickname of US State" , "Indians" , "US native" , "Native American - French hoodlum" , "N. American native; French ruffian" .)