Have a look at Runtime.exec() Javadoc
Process p = Runtime.getRuntime().exec("ssh myhost");
PrintStream out = new PrintStream(p.getOutputStream());
BufferedReader in = new BufferedReader(new InputStreamReader(p.getInputStream()));
out.println("ls -l /home/me");
while (in.ready()) {
String s = in.readLine();
System.out.println(s);
}
out.println("exit");
p.waitFor();