(PHP 5 >= 5.2.0, PECL zip >= 1.4.0)
ZipArchive::setCommentIndex — Set the comment of an entry defined by its index
Set the comment of an entry defined by its index.
indexIndex of the entry.
commentThe contents of the comment.
   Returns TRUE on success or FALSE on failure.
  
Example #1 Open an archive and set a comment for an entry
<?php
$zip = new ZipArchive;
$res = $zip->open('test.zip');
if ($res === TRUE) {
    $zip->setCommentIndex(2, 'new entry comment');
    $zip->close();
    echo 'ok';
} else {
    echo 'failed';
}
?>