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) {
        }

Your code is fine, but the problem is inside the batch file.

You have to show the content of the bat file, your problem is in the paths inside the bat file.

Following is worked for me

File dir = new File("E:\\test");
        ProcessBuilder pb = new ProcessBuilder("cmd.exe", "/C", "Start","test.bat");
        pb.directory(dir);
        Process p = pb.start();