Applting for a single entry visa in Tokyo

We are flying into Shanghai from the uk, then to Hong Kong, then to Xian, then to Tokyo and back to Shanghai. I have been told today that the tourist multiple entry will only cover 2 entrances into mainland and that we will therefore need to apply for a single entry one to get back onto
shanghai in Tokyo. We are only in there for a few nights will it be possible to get one back in time and is this a straightforward process?