Take a look at your web server's log, there's likely to be a helpful error message in there somewhere. As a first shot, try using an absolute path in your system() call, e.g.

system("/usr/bin/java","JavaClassFile");
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(adjust path as appropriate). Note that there's probably a better way to reach your goal unless this is just a quick'n dirty solution you're developing (for example Inline::Java allows you to put Java code directly into your perl script).