You can use the core opendir and readdir functions. I think you should read file by file (due the number of files) and move them using File::Copy.

use File::Copy;
use File::Spec;

my $filecount = 0;
my $dircount = 0;

opendir my $basedir, "." or die $!;
while (my $file = readdir($basedir)) {
    next if $file =~ /^\.\.?$/ or -d $file;
    my $targetdir = "dir${dircount}";
    do { mkdir $targetdir or die $!; } unless -d $targetdir;
    move($file, File::Spec->catfile($targetdir, $file)) or do { warn $
+!; next; };
    if ($filecount > 999) {
        $filecount = 0;
        $dircount++;
    }
}
closedir $basedir or die $!;
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