The PHP ftp_chmod() function sets permissions on the specified file via FTP.

<?php
// connect and login to FTP server
$ftp_server = 'ftp.example.com';

$ftp_conn = ftp_connect($ftp_server) or die('Could not connect to ' . $ftp_server);
$login = ftp_login($ftp_conn, $ftp_username, $ftp_userpass);

$file = '/test/my-file';

// try to set read and write for owner and read for everybody else
if (ftp_chmod($ftp_conn, 0644, $file) !== false) {
    echo 'Successfully chmoded ' . $file . ' to 644.';
}
else {
    echo 'chmod failed.';
}

// close connection
ftp_close($ftp_conn);
?>

// sets file permissions

ftp_chmod(ftp_conn, mode, file)