Voltage regulation for very low power
If cost is not too much of a concern, a switching regulator such as the LTC3388 may suffice. It draws well under 1uA (Iq, no-load) with a 12V input. 

Your average consumption (at 3V) will be about 3.2uA, assuming the 0.1% duty cycle number is accurate, so the average from your 12V battery should be less than 2uA (but read the datasheet carefully). 

A simpler and potentially cheaper solution would be to use a linear CMOS regulator with (say) 1uA Iq. The average current draw would then be ~4.2uA from the 12V battery. That may in fact be much less than the self-discharge current of the 12V battery so it might not make much difference (to the battery life) which you choose, despite the more than 2:1 decrease in efficiency.