Military officer in charge has stomach upset (5)
I believe the answer is:
colic
'stomach upset' is the definition.
'military officer in charge' is the wordplay.
'military officer' becomes 'col' (colonel**).
'in charge' becomes 'ic'.
'col'+'ic'='COLIC'
'has' is the link.
(Other definitions for colic that I've seen before include "Severe stomach pain" , "Intestinal infection" , "Abdominal pain, especially in infants" , "Abdominal pain from wind or obstruction" , "Gastric pain" .)