Home Office head stops just over a hundred masses (3,6)
I believe the answer is:
hoi polloi
'masses' is the definition.
(Greek term for the common people)
'home office head stops just over a hundred' is the wordplay.
'home office' becomes 'HO' (abbreviation).
'head' becomes 'poll' (dialect term for the head).
'stops' means one lot of letters goes inside another (stopping can mean blocking a gap).
'just over a hundred' becomes 'IOI' (IOI resembles 101).
'poll' put within 'ioi' is 'ipolloi'.
'ho'+'ipolloi'='HOI-POLLOI'
(Other definitions for hoi polloi that I've seen before include "The masses (Greek)" , "Riff-raff" , "The common people generally" , "ordinary people" , "commoners" .)