I tried a simple Cwd script with a simple Net::SSH::Perl script. Worked for me:

#!/usr/bin/perl

use strict;
use warnings;
use Cwd;

my $dir = getcwd;
print $dir, "\n";
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The Net::SSH::Perl script:

#!/usr/bin/perl

use strict;
use warnings;
use Net::SSH::Perl;

use constant {
    HOST      => 'localhost',
    USER      => 'user',
    PASSWORD  => 'password',
};
   
my $ssh = Net::SSH::Perl->new(
    HOST,
    port     => 22 || 'ssh',
    protocol => 2,
    debug    => 1,
);
$ssh->login(USER, PASSWORD);

my ($stdout, $stderr, $exit) = $ssh->cmd(
    'perl /root/Desktop/cwd.pl');
print $stdout, "\n";

exit;
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