The following is probably faster (especially for large amounts of data), and it sorts the ports numerically. Your solution oddly sorted them alphabetically.

sub sort_by_ip {
   return
   map { substr($_, 4) }
   sort
   map { pack("C4a*", split(/\./), $_) }
   @_;
}

my %data;

while (<DATA>) {
    chomp;
    my ($src, $dest, $dst_port) = (split)[5,9,10];
    $data{$src}{$dest}{$dst_port}++;
}

foreach my $src      (sort_by_ip         keys %data                ) {
foreach my $dest     (sort_by_ip         keys %{$data{$src}}       ) {
foreach my $dst_port (sort { $a <=> $b } keys %{$data{$src}{$dest}}) {
   print "$src $dest $dst_port $data{$src}{$dest}{$dst_port}\n";
}}}
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