Yes, you should probably consider using Getopt::Long.

But, as for your script, it seems that the problem is the following:

          if (@ARGV > 0) {
                if ( $ARGV[0] eq "-c") {
                    if (  ! -e "$ARGV[1]" ) {
                        print "Provided xml file doesnot exists\n";
                        }
                    elsif ( -f "$ARGV[1]") {
                        $controlfile = $ARGV[1];
                        parse_xml();
                        update_exports();
                        }
                    }
        else { #...
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If (@ARGV > 0), then the number or arguments should really be 2 (you need 0 or 2 arguments, the option and the file name), so that if (@ARGV == 1) (only one argument) it is also an error, but your code is not checking that, hence the problem when you pass the option flag but not the file name.

In brief, if (@ARGV > 0), then you should check that you have (@ARGV == 2), or else call the usage() sub.