ISM code deals with safety and pollution prevention. Everything in ISM code is about ship safety and preventing pollution into sea. Master's overriding authority too is on issues concenring Ship's safety and pollution prevention.
When we use the word Over-ride, it automatically involves two situations or decisons which are contradictory to each other. For example, if Master feels he should take some decison for the safety of the ship but there is nobody who is stopping him to take this decison, it cannot be said that he has used his overriding authority.
If Master is doing everything as per his duties defined in the SMS, he is not overriding anything. He is just doing his duties.
Let us say, Master arrives at a port and decides that he need to anchor for complying with crew rest hours. Is he over-riding anything ? Has he used his over-riding authority ?
No, he hasn't. SMS manual would say that it is Master's duty to ensure that crew of the ship are well rested.
Now let us see some examples of Master's over-riding authority.
Let is say the charterers of the ship advise Master to take a shorter route that is expected to have very heavy weather. Master is not comfortable with that route and wants to take longer but safer route. Charterers and ship owner are trying to force their decision on master. Master can advise them that he is using his Over-riding authority.
Another example would be where master is asked to berth the vessel with very less under keep clearance. Even if company has evaluated the situation and granted permission to berth with lesser UKC than minimum required by the company, master can use his over-riding authority to not berth the vessel.