This is how to proceed.
The Minister who wants you to lose the sensitive document - which may detail allegations against Ministers - will give you a special wink when he passes it over. "Store this very carefully" he will say and you must pay attention to his face.
He will give no more clues and he will never put an instruction in writing. It is up to you to use your initiative. Being a civil servant this is a very difficult thing to do but other more senior servants of the Crown will help.
Once you are assured that the file needs to be destroyed you have a number of choices.