Your error has nothing to do with Javascript. You're doing this:

$cgi->(...)

That is the syntax for executing a coderef. But $cgi is not a coderef (it's presumably a CGI object).

It's not exactly clear what you want to happen here, but you may have meant:

print $cgi->start_html(
   -title  => 'Pop-up Window',
   -script => {
      -language => 'javascript',
      -type     => 'text/javascript',
      -src      =>'http://s-internal.xxxx.com/xxxx/pop-up.js',
      }
    );
[download]

And by the way, Perl will not be "calling" the Javascript file. It will simply output an HTML <script> element which asks the browser to download and execute the script.

Aside: It is certainly possible (via things like JE or JavaScript::SpiderMonkey) for Perl to call javascript code, but that's definitely not what you want here.