You could treat it as string, transform to final version and do eval:

#!perl -l

@strings = <DATA>;

for(@strings)
{
    chomp;
    s/,/'}{'/g;
    s/^/\$hash{'/;
    s/$/'}++/;
    print "eval $_";
    eval $_;
}

use Data::Dumper;
print Dumper \%hash;

__DATA__
string1,string2,string3,string4
string3,string4
string1,string2,string3
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Output:

c:\>test.pl
eval $hash{'string1'}{'string2'}{'string3'}{'string4'}++
eval $hash{'string3'}{'string4'}++
eval $hash{'string1'}{'string2'}{'string3'}++
$VAR1 = {
          'string3' => {
                         'string4' => 1
                       },
          'string1' => {
                         'string2' => {
                                        'string3' => 5393161
                                      }
                       }
        };
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But as you can see there is a problem to solve: 'string3' => 5393161 which was created as reference to hash, but then replaced by value. What do you want to do in such situation?