Answer
(Fatwa: 278/170/D=1432)
If you are the owner of the mill, this commission shall be lawful for you; because it is like “decreasing the fixed price”, (the person who has taken the goods from you is returning you from the original price willingly). But, if you work as manager, you are amin and wakil (trustee and agent), hence it shall not be lawful for you to take this commission, rather it shall be necessary for you to return this amount of commission to the real owner as being wakil so that the company can gain more through you.
قال رسول الله صلى الله عليه وسلم … هلا جلس في بيت أبيه أو في بيت أمه ؛ فينظر أيهدي له أم لا . مشكاة المصابيح (156)
Allah (Subhana Wa Ta’ala) knows Best
Darul Ifta,
Darul Uloom Deoband