I am running my web app using Perl/CGI on Apache server (Not Tomcat) under Linux.

Why are you not using a web container like Tomcat? Or JBoss? Or Geronimo?

This is a rather bizarre implementation to say the least. Not one that I'd recommend in any form of production code. I just did a super search and came up empty, but somewhere in the Monastery catacombs exists a troubleshooting checklist for issues with CGI. Off the top of my head I'd suggest checking the following:

• File permissions: quite frequently the CGI environment is running as a user other than what you are running as when executing from the command line.
• Server Logs: Usually a font of information as to "why this ain't working."
• Put debugging code into your CGI

To that last point I always recommend you run the following code as a CGI (or some form of it) and quickly remove it from your production environment:

#!/usr/bin/perl -w 
use strict;
use CGI qw/ :all /;
use CGI::Carp qw/ fatalsToBrowser /;

print header,start_html;
print h1('Environmental Variables');
print ul(map{li($_ . ": " . $ENV{$_})} sort keys %ENV);
print h1('CGI Parameters');
print ul(map{li($_ . ": ". param($_))} sort param());
print end_html;
exit(0);
[download]

This code will give you some idea of what is going on in you CGI environment.