Most Linux/Unix systems I have worked with over the last few years do not enable Telnet since it has little or no security. The norm these days is to use SSH which creates an encrypted channel and SSH is available for just about all OS and is normally trivial to install. You will probably find it is already installed.
There are many Java SSH clients (Google will find them) but my preference is for JSch from http://www.jcraft.com/jsch/. Using it you can either execute a single command or pass multiple commands through a shell 'stdin'. Depending on your security requirements you can either use (username, password) authorization or public key certificate authorization; my preference is always for public key certificate authorization.