My Malaysian tourist visa is about to expire, and my work visa is still being processed, but I can't come down until the tourist visa expires. What should I do?

Did you get the work visa yourself, or did you ask an agent to help you get it?

Basically, when your tourist visa expires, you have two choices. Either you leave the country or you apply for an extension. I suggest that you don't overstay, or even if your work visa is approved, it is estimated that the Immigration Bureau will refuse to give you a work permit and a long-term residence permit because of your overstaying.