A minor change to your code...

my %MSISDN=();

#populate the subscription list to hash MSISDN

        open(FILE,"/tmp/subscription_list") || die "Unable to open sub
+scription file";
        %MSISDN = %{ file_merge(\%MSISDN) };
        close(FILE);

my  %Calls=();

#populate the usage types to hash Calls

       open(FILE1,"/tmp/Call_Det")|| die "Unable to open call_details 
+file";
       %Calls = %{ file_merge(\%Calls) };
       close(FILE1);
}

sub file_merge
{
## take from @_ (the args passed to the subrtn)
my $hash_ref = shift; 
while (<>) {
  chomp;
  my ($key, @values) = split /-/, $_;
  push @{$hash_ref{$key}}, [ @values ];
}
return $hash_ref;
}
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But you would be better off passing in the filepath, doing the reading and parsing in your sub and passing back the hash ref... see below by davorg...