Try this:
Calendar nowCal = (however you get/set the time you care about, as a Calendar)
long now = nowCal.getTimeInMillis();
long millis_today = now % 86400;
long millis_in_days = (nowCal.get(Calendar.DAY_OF_WEEK) - Calendar.SUNDAY) * 86400L;
long time_since_midnight_sunday = millis_in_days + millis_today;