Tool in church lies broken (6)
I believe the answer is:
chisel
'tool' is the definition.
(chisel is a kind of tool)
'church lies broken' is the wordplay.
'church' becomes 'ch' (common abbreviation).
'broken' is an anagram indicator.
'lies' with letters rearranged gives 'isel'.
'ch'+'isel'='CHISEL'
'in' acts as a link.
(Other definitions for chisel that I've seen before include "Carpenter's tool for shaping wood" , "Carpentry tool" , "Flat steel tool with a cutting edge" , "Sculpting tool" , "Wood, stone or metal-cutting tool" .)