If there is an unavoidable mandate to keep the "home-grown database" in operation (e.g. because some critical activity is intricately dependent on using that Java command line interface tool, and you can't change that), then a worst-case-kluge scenario for a perl interface might be to write a wrapper module that simply runs your java command line tool in some sensible way.

But I'd really want to check whether it would be possible to replace this home-grown DB with something else that has broader support and better (more flexible) accessibility. Just use the existing java command line tool to dump out the current contents, load them into some other DB, and move on.