For anyone else that may of come across the same problem here is the answer that i stumbled on eventually.
final HttpContext httpContext = jettyServer.createContext("/service");
com.sun.net.httpserver.BasicAuthenticator a = new com.sun.net.httpserver.BasicAuthenticator("") {
public boolean checkCredentials (String username, String pw)
{
return username.equals("username") && pw.equals("password");
}
};
httpContext.setAuthenticator(a);
endpoint.publish(httpContext);//access by path
You can expand the checkCredentials for something a bit more sophisticated of course, but this shows the basic working method.