Thanks to those that looked into it.
The issue was something to do with the booking system. It seems the schedule had not been plugged into it properly.
I called Malaysia Airlines directly on the phone and even they couldnt give me a price!
They logged the fault and had it rectified later that day.
Interestingly, while the fault was still there a flight COULD be booked through the mobile website, but fares were showing at about 300,000 yen (over US$3000) one way for economy!