As far as I understand it's not as simple as using JSSE. Secure FTP (sftp) tunnels the FTP connection over ssh (Secure SHell).
Although there are a number of open sftp implementations available, there is no Java version as far as I know. You could have a look at
ISNetworks' SSH, which appears to be derived off the old GPL version of MindTerm. It supports only SSH1, which may well be a problem. It also only supports ssh and scp. But it might help.
- Peter