I have some cgi scripts and I hosted it in apache.

This is working file in browser IE but in other browsers like chrome/firefox, only the code is shown and not executed properly.

How can I overcome this compatibility issue in cgi ??

It is not a compatibility issue in CGI, it is an Internet Explorer compatibility issue.

In most similar cases I've seen, the actual problem is that either the CGI program is not executable, or Apache is not correctly configured to execute the CGI program.

I've never seen a case where one browser does cause the server to execute the CGI, where other browsers do not. It is possible to achieve by using some rather esoteric setenvif/browsermatch directives, but I've never seen in real life.

What I have seen, over and over, is stale caches. In IE, you need to press Ctrl+F5 (I think) to actually reload the page; basic F5 just reloads it from IE's own cache. Go to another page, clear your caches, and restart IE, to see if that was your actual problem.