is it is possible to disable the windows keys using java

You can use JNA to achieve this.

Include jna.jar and platform.jar on the classpath and create the following class.
This class disables left windows key (0x5B) and right windows key (0x5C). So you can add other codes at the switch case statement.

Call KeyHook.blockWindowsKey() as soon as possible when your application starts.
On the other side, call unblockWindowsKey() at app shutdown.

Since the code is only executed when isWindows() is true, you can always call KeyHook.blockWindowsKey(), even when running on another OS.

    import com.sun.jna.platform.win32.Kernel32;
    import com.sun.jna.platform.win32.User32;
    import com.sun.jna.platform.win32.WinDef.HMODULE;
    import com.sun.jna.platform.win32.WinDef.LRESULT;
    import com.sun.jna.platform.win32.WinDef.WPARAM;
    import com.sun.jna.platform.win32.WinUser.HHOOK;
    import com.sun.jna.platform.win32.WinUser.KBDLLHOOKSTRUCT;
    import com.sun.jna.platform.win32.WinUser.LowLevelKeyboardProc;
    import com.sun.jna.platform.win32.WinUser.MSG;


    public class KeyHook {
        private static HHOOK hhk;
        private static LowLevelKeyboardProc keyboardHook;
        private static User32 lib;

        public static void blockWindowsKey() {
            if (isWindows()) {
                new Thread(new Runnable() {

                    @Override
                    public void run() {
                        lib = User32.INSTANCE;
                        HMODULE hMod = Kernel32.INSTANCE.GetModuleHandle(null);
                        keyboardHook = new LowLevelKeyboardProc() {
                            public LRESULT callback(int nCode, WPARAM wParam, KBDLLHOOKSTRUCT info) {
                                if (nCode >= 0) {
                                    switch (info.vkCode){
                                        case 0x5B:
                                        case 0x5C:
                                            return new LRESULT(1);
                                        default: //do nothing
                                    }
                                }
                                return lib.CallNextHookEx(hhk, nCode, wParam, info.getPointer());
                            }
                        };
                        hhk = lib.SetWindowsHookEx(13, keyboardHook, hMod, 0);

                        // This bit never returns from GetMessage
                        int result;
                        MSG msg = new MSG();
                        while ((result = lib.GetMessage(msg, null, 0, 0)) != 0) {
                            if (result == -1) {
                                break;
                            } else {
                                lib.TranslateMessage(msg);
                                lib.DispatchMessage(msg);
                            }
                        }
                        lib.UnhookWindowsHookEx(hhk);
                    }
                }).start();
            }
        }

        public static void unblockWindowsKey() {
            if (isWindows() && lib != null) {
                lib.UnhookWindowsHookEx(hhk);
            }
        }

        public static boolean isWindows(){
            String os = System.getProperty("os.name").toLowerCase();
            return (os.indexOf( "win" ) >= 0);
        }
    }