I\'m copying this question from over here: http://getsatisfaction.com/cyberduck/topics/can_i_use_sudo_over_sftp_with_cyberduck
I am having the same issue and finding it
I upload the file with cyberduck to a folder where i can write to (e.g. the home folder of the cyberduck connected user). Then i login to the machine via ssh and sudo mv the file to the desired destination folder.