I doubt the number of keys is the problem. This script runs fine for me with 100000 keys.... you could have millions if you have the ram.

#!/usr/bin/perl
use warnings;
use strict;

my %hash;

for(1..100000){
 $hash{$_}= 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa';
}

print "check mem and hit enter\n";
<>;
[download]

For 100000 keys I use 14megs. 1000000 keys uses 124megs. Show us a simplified example which demonstrates the problem.