You'll need to change statement modifiers:

do_something() if ...
[download]

to standard conditionals:

if ($some_condition) { 
    do_something();
}
[download]

to be able to use else statements as suggested by Corion:

   if ($intermediate_array[12] eq "GSM") {               
       if (grep { /^\Q$intermediate_array[11]\E$/ } @subscriber_error 
+) {
           $MO_userdep_error++ ;
       } elsif (grep { /^\Q$intermediate_array[11]\E$/ } @network_erro
+r) {
           $MO_network_error++;
       } else {
           $MO_system_error++  if grep { /^\Q$intermediate_array[11]\E
+$/ } @system_error;
       }
   }
[download]

As mentioned by Athanasius, replacing grep by the any function of List::Utils module is also likely to speed up your program.

Also, testing for string equality might be slightly faster than a regex.