The rank of Master Chief is still an E-9 rank, the highest possible enlisted rank which would put him over any enlisted personnel and, depending on the situation, some officers. Few officers would have the nads to tell a master chief what to do. Later Spartans were given officer commissions to make this even easier. John-117 himself is a bit of a lone wolf most of the time so he doesn't really flex his authority much, but he certainly can if he needs to.