We are travelling into Hong Kong for two days and then on to Shanghai for a day on a cruise.

Dear Anne, you don't need the entry permit for HK as an Australian passport holder. In normal cases, you need to apply for one to Shanghai. However, if you stay in mainland China for less than than 24 hours, it's possible that you qualify for the 24-hour free transit policy so that the entry permit is not necessary either. You can check whether your route is eligible for this policy.