Use ssh-copy-id on a non-default port

ssh-copy-id has known problems with handling non-standard ports (e.g. connecting to a different port than 22). To overcome this issue, use a command like:

$ ssh-copy-id "user@host -p 6842"

Source:http://it-ride.blogspot.com/2009/11/use-ssh-copy-id-on-different-port.html