I glossed over a few details, but the main reasons are that a.) current interest rates are lower in Japan than the U.S. to begin with (BOJ benchmark rate is 0%, vs. Fed rate of 1.25%) and b.) the most common long-term Japanese mortgage is actually a 35-year mortgage partially guaranteed by the government. The 35-year term (vs. 30 years) knocks the interest rate down a bit, and the partial guarantee (similar to a U.S. FHA or VA loan, but the buyer still needs a 10-20% downpayment) reduces it even further.