The clunky way I've used in the past was basically to call Runtime.exec(String[]) like this:

String[] command = new String[]{"perl", scriptName, arg1};
            try {
                Runtime r = Runtime.getRuntime();
                Process p = r.exec(command);
                // Read the results
                InputStream in = p.getInputStream();
                // ...
                in.close();
                
            } catch(Exception e) {
                e.printStackTrace();
            }
[download]

The downside is that (at least on a Unix-like system) the Runtime#exec() call has to fork a copy of the Java VM, so you need plenty of RAM to get away with this.

I've sure there must be some cleverer way using JNI, but I've never got my head around it.