I personally think you'll be much better off renting for at least the first 6 years. You have no idea where you'll be working, and gaijin get canned from seemingly permanent positions without little consideration to their personal circumstances: wife, family, mortgage. etc.
To just balance things out more objectively, you're going to need to be on AT LEAST a three-year renewable work visa before the banks will even touch you AFA a loan is concerned. Preferably you'll have permanent residency, if single, or be on your second three-year spouse visa if married to a Japanese national. In my own case I secured a joint loan for 3500 man yen together with my wife whilst on my second three-year spouse visa. But don't take that as a standard. I've been self-employed for 8 years and have a very, very solid financial paper trail in Japan (in other words I used an accountant!). From what friends have told me, the loan rules have been tightened up somewhat and permanent residency status is becoming a standard requirement for house loans.
BTW I don't live anywhere near a large city. My house loan is a little higher than average - but I have things like a classroom included, as well as a central air-conditioning system. Plus I didn't have to pay for the land (1500 man estimate) so we spent more on the house.
I rented, together with my wife, for six years and saved up plenty. Paying 1000 man upfront is pretty normal when building a house. And YES the prices sound outrageous by North American standards, but I'm British – and 250,000 quid for a four-bedroom, detached house, with 6-car parking, central-air-conditioning (not that we have that in the UK), etc. would be on the cheap side. When you factor in an interest rate of about 1.8% here in Japan then it sounds very cheap.