If Apache (or whoever) tells you that they can't open a script because they get permission denied, a first look would be at the permissions of all files involved and at the user(s) that the scripts are being executed as:

1. Determine user (and uid) of the user trying to run the script. Most likely this will either be the httpd user or the user your web server is configured to run CGI scripts as.
2. Permissions of the script and all directories above the script. The directories should ideally all have read and execute permissions.

3. Permissions of the interpreter named on the first line of the script. The script must start with #!/usr/bin/perl -w or something like that. Check that the interpreter used exists and that the permissions on the interpreter executable and the containing directories also match the CGI users set.

As you don't show any code or configuration, it's hard to give more concrete advice. Maybe the error log files of your webserver tell you some more details.