Secure FTP with org.apache.commons.net.ftp.FTPClient

First, make sure you understand a difference between FTPS (Secure FTP) and SFTP:
FTPS versus SFTP versus SCP

---

• If you need FTPS (aka Secure FTP or FTP over TLS/SSL), you can use FTPSClient class from Apache Commons library instead of FTPClient.

• If you need SFTP (over SSH), you need a different library. See:
  How to retrieve a file from a server via SFTP? or
  Java SFTP Transfer Library.

Apache FTPClient doesn't support SFTP at the moment. However, you can use JSch - Java Secure Channel.

Onkar Joshi goes into more details of the library to use for FTP, SFTP, FTPS file transfer in Java.

An example of using JSch to transfer files with SFTP is as follows:

    ...

private static final Logger logger = Logger.getLogger(YourClass.class.getName());

public boolean sendDataViaSFTP(String contents) throws Exception {
    String hostname = "<FTP hostname/IP>";
    String username = "<FTP username>";
    String password = "<FTP password>";
    String remoteDirectory = "<FTP remote directory>";
    int ftpPort = 22;

    logger.info("***   Creating FTP session.   ***");
    JSch jsch = new JSch();
    Session session = null;
    Channel channel = null;
    ChannelSftp c = null;

    //Now connect and SFTP to the SFTP Server
    try {
        //Create a session sending through our username and password
        session = jsch.getSession(username, hostname, ftpPort);
        logger.info("***   FTP Session created.   ***");
        session.setPassword(password);

        //Security.addProvider(new com.sun.crypto.provider.SunJCE());
        //Setup Strict HostKeyChecking to no so we dont get the
        //unknown host key exception
        Properties config = new Properties();
        config.put("StrictHostKeyChecking", "no");
        session.setConfig(config);
        session.connect();
        logger.info("***   Session connected.   ***");

        //Open the SFTP channel
        logger.info("***   Opening FTP Channel.   ***");
        channel = session.openChannel("sftp");
        channel.connect();
        c = (ChannelSftp) channel;

        //Change to the remote directory
        logger.info("***   Changing to FTP remote dir: " + remoteDirectory + "   ***");
        c.cd(remoteDirectory);

        //Send the file we generated
        try {
            String filename = "myfile.txt";

            logger.info("***   Storing file as remote filename: " + filename + "   ***");

            ByteArrayInputStream bis = new ByteArrayInputStream(contents.getBytes());
            c.put(bis, filename);
            return true;
        } catch (Exception e) {
            logger.info("***   Storing remote file failed. " + e.toString() + "   ***");
            throw e;
        }
    } catch (Exception e) {
        logger.info("***   Unable to connect to FTP server. " + e.toString() + "   ***");
        throw e;
    } finally {
        //
        //Disconnect from the FTP server
        //
        try {
            if(session != null)
                session.disconnect();

            if(channel != null)
                channel.disconnect();

            if(c != null)
                c.quit();
        } catch (Exception exc) {
            logger.severe("***   Unable to disconnect from FTP server. " + exc.toString()+"   ***");
        }

        logger.info("***   SFTP Process Complete.   ***");
    }

}

...

Try Java Secure Channel

It supports SFTP

http://www.jcraft.com/jsch/

Example can be found here

You can use org.apache.commons.net.ftp.FTPSClient instead of org.apache.commons.net.ftp.FTPClient to have secure ftp http://commons.apache.org/proper/commons-net/apidocs/org/apache/commons/net/ftp/FTPSClient.html