Agreement thus broken ultimately by academic institution (6)
I believe the answer is:
unison
'agreement' is the definition.
(unison is a kind of agreement)
'thus broken ultimately by academic institution' is the wordplay.
'thus' becomes 'so' (synonyms).
'ultimately' indicates one should take the final letters.
'by' says to put letters next to each other.
'academic institution' becomes 'uni' (university).
The last letter of 'broken' is 'n'.
'so'+'n'='son'
'son' after 'uni' is 'UNISON'.
(Other definitions for unison that I've seen before include "Togetherness - TUC member" , "In agreement - like sound of choir" , "Sameness in pitch" , "Complete agreement, harmony" , "Unanimity" .)