Set the “parent” parameter as 0.
$args = array(
'parent' => 0,
'post_type' => 'custom-post-type',
'number' => '1',
'orderby' => 'date',
'order' => 'DESC'
);
$comments = get_comments($args);
foreach($comments as $comment) :
echo($comment->comment_author . '<br />' . $comment->comment_content);
endforeach;