I agree male organ is way short (4)
I believe the answer is:
amen
'i agree' is the definition.
('amen' might be said to indicate agreement)
'male organ is way short' is the wordplay.
I cannot quite understand how this works, but
'male' could be 'm' (common abbreviation) and 'm' is located in the answer.
'way' could be 'n' (Compass direction - North) and 'n' is located in the answer.
The remaining letters 'ae' is a valid word which might be clued in a way I don't see.
This may be the basis of the clue (or it may be nonsense).
Can you help me to learn more?
(Other definitions for amen that I've seen before include "Last word of prayer" , "statement of affirmation" , "So let it be" , "Word at the end of a prayer" , "prayer's ending" .)