One more entry needed. Can I do it when in Japan? Do I have the time?

I'm an Italian citizen and I'm, presently in Beijing with a two entry Visa (three months each). On April the 20th I'll come to Japan and I'll fly back to Beijing on the 28th. However, at the end of May I would like go once more out of China (Malaysia), so I guess I'll need another one. Can I do this when I'm in Japan?
Also, I'll be in Tokyo 20th-23rd; on the 24th I'll have to move to Kyoto. Do I have the time to do it?
Thank you