I was trying to use the great data in this thread but found at my 1.6.7 level the WDT_disable() call is no longer in the arduino_due_x\variant.cpp file.
What seems to have happened is the introduction of watchdog.cpp and watchdog.h in arduino\hardware\sam\1.6.7\cores\arduino directory.
Within the watchdog.cpp there is a watchdogSetup() defined so that it has a weak reference to a WDT_disable(WDT); call. This stops the watchdog timer interupting sketches that dont use it.
So if you want to use the watchdog timer at this level, enable it by putting the following in your sketch.
void watchdogSetup(void) { }
This function can be empty as shown and creates a strong reference thus overiding the WDT_disable(WDT).
Then you should be able to use the "watchdog.h" or "wdt.h" calls.