See Watching Long Processes Through CGI. If your webserver is purely written in Perl, you will have to do the hard/long work in a background process or thread, or use POE or Coro.

<div id="waitBox" style="background-color: #d6e7fe; font-family:Arial,
+Helvetica, sans-serif; font-size: 10pt;
font-weight: bold;color: #000000;text-align: left; position:absolute; 
+border: thin solid #1A448E; padding: 5px;
display: none; z-index: 3000; width:250px; height:75px;"></div>

<script type="text/javascript">
function showWait(status){
        var object=document.getElementById('waitBox');
        if(status){
                object.style.left = (document.body.clientWidth - 250) 
+/ 2;
                object.style.top = document.body.scrollTop + (document
+.body.clientHeight - 75) / 2;
                object.style.display = "block";
                object.innerHTML='<br><center>Please wait while your s
+earch is being performed...</center>';
        }else{object.style.display = "none";}
}
</script>
<form action="script.pl" method="post" name="form1">
<input type="button" onclick="showWait(1);this.form.submit();" value="
+Search">
</form>
[download]

Although I have not yet understood this (it is late at night here!) I read it as offering the user a button, which appears somewhere when the submit (done from a separate frame) is clicked. Not exactly what I had in mind, but maybe it can be adopted. Really, I would like to keep the user updated as to what the main script is doing (and can take a variable amount of time which I cannot estimate in advance). I would have preferred to stay purely in Perl, not having much Javascript knowledge.