Run batch file from Java code

Rather than Runtime.exec(String command), you need to use the exec(String command, String[] envp, File dir) method signature:

Process p =  Runtime.getRuntime().exec("cmd /c upsert.bat", null, new File("C:\\Program Files\\salesforce.com\\Data Loader\\cliq_process\\upsert"));

But personally, I'd use ProcessBuilder instead, which is a little more verbose but much easier to use and debug than Runtime.exec().

ProcessBuilder pb = new ProcessBuilder("cmd", "/c", "upsert.bat");
File dir = new File("C:/Program Files/salesforce.com/Data Loader/cliq_process/upsert");
pb.directory(dir);
Process p = pb.start();

try following

try {
            String[] command = {"cmd.exe", "/C", "Start", "D:\\test.bat"};
            Process p =  Runtime.getRuntime().exec(command);           
        } catch (IOException ex) {
        }