Yes. Although if the client machine is running Windows I'm not quite sure how. Another *n*x box could simply Runtime.exec("/usr/bin/ssh"). I think putty may have a command-line option as well, but I'm not sure. I know the cygwin package does - it's the same basic ssh program as Linux uses.
Doing a Runtime.exec of a shell program can be a little tricky because it's conversational. You have to capture stdin and stdout and use them as your conversation channels. It's easier when you just want to remotely execute a single non-interactive program/script via ssh, since you only have to worry about the output and not the input.
An IDE is no substitute for an Intelligent Developer.