Well I could think of a quick way using eval, but I won't. (update hint: it'd involve replacing the dots with "}{".) So the only other option is to "walk the chain". Note that your concept is intrinsically unsafe. If you add a parameter with name 'a.b', the whole thing will blow up.

use CGI;
my $cgi = CGI->new( 'a.b.c=3&a.b.c=4&x.y=4' );

my $args = {};

my @names = $cgi->param;
foreach my $name (@names) {
    my $p = $args;
    my @keys = split /\./, $name;
    for my $i (0 .. $#keys-1) {
        $p = $p->{$keys[$i]} ||= {};
    }
    my @values = $cgi->param($name);
    $p->{$keys[-1]} = @values==1 ? $values[0] : \@values;
}

use Data::Dumper;
$Data::Dumper::Indent = 1;
print Dumper $args;
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Result:

$VAR1 = {
  'x' => {
    'y' => '4'
  },
  'a' => {
    'b' => {
      'c' => [
        '3',
        '4'
      ]
    }
  }
};
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Update For the cases where this would blow up, there is no solution. So the only reasonable thing to do is to catch this if it is bound to happen, for example by checking the reference type using ref, and complain in a nice, preferably opaque way.