You could use a hash of hashes and (if your range is fixed) - use keys of either the high or low values.

For instance, if you were going to go low values, your structure would look like $hash->{123}->{456} for the example.

 my $range = 1;
 my $hash = {};
 while (<>) {
   chomp;
   my ($num1, $num2) = split ' ',$_; # key the numbers
   my $int_num1 = int( $num1 );      # drop the decimal

   # this will create the correct key for an integer range
   # e.g. if you had a range of 5, this would result in
   # 120 being the first bucket

   my $key1     = $int_num1 - ($int_num1 % $range);

   # combined steps for key2
   my $key2 = int($num2) - (int($num2) % $range);

   $hash->{$key1}->{$key2}++;
 }

 # now you can get your indices

 foreach my $range1 ( keys %$hash ) {
   foreach my $range2 ( keys %{$hash->{$range1}} ) {
     print $range1."-".($range1+$range);
     print " ";
     print $range2."-".($range2+$range);
     print " ";
     print $hash->{$range1}->{$range2};
     print "\n";
   }
 }
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This is untested, but I think (hope) it gives you at least an idea of one way to do it. Of course you can make it more efficient, shorter, etc.