Reproductive organ's extremely short, I agree (6)
I believe the answer is:
stamen
'reproductive organ's' is the definition.
(plant organ)
'extremely short i agree' is the wordplay.
'extremely' suggests removing the centre (extreme, outside letters only).
'i agree' becomes 'amen' ('amen' might be said to indicate agreement).
'short' with its middle taken out is 'st'.
'st'+'amen'='STAMEN'
(Other definitions for stamen that I've seen before include "Bit of a bloomer" , "Male part of flower" , "Flower pollen carrier" , "Fertiliser" , "Male reproductive organ of a flower" .)