If your shaken runs out and the car is not worth putting through shaken again (or if it has a breakdown while the shaken is still in effect that would be too expensive to fix), then you are required to dispose of the car through the "haisha" process. If the car is still driveable, it's best to take it yourself to the junk yard, as this will save you some money. Otherwise, you'll have to have it towed off at considerable expense. The best place I know of is a junk yard in "Kise", about 500 m south of where Tsuchiura-Gakuen Sen crosses over the Joban Expressway, just west of the access road along the expressway. In the "good old days" of 10 years ago or so, junk yards would actually pay you several thousand yen for your car. Now, you generally have to pay them to take it off your hands. This junk yard usually charges no more than ¥5000.
You will, of course, occasionally see abandoned cars along back streets where irresponsible people have simply left them. The license plate has been removed, and typically, all identifying numbers have been filed off to prevent the police from identifying the culprit. The net result, of course, is that our tax money then has to be spend to haul it away. That seems like a lot of trouble to go through to avoid paying a small fee, in addition to just being plain unethical.
Presumably, these people have turned in their license plate so that they won't continue to be sent a car tax bill each May. This is, of course, part of the "haisha" process. After you have properly disposed of the car, you take the license plate to the same place where the shaken inspections are made. There is a form you have to get in the building closest to the expressway along with a ¥350 stamp. The properly filled in form, along with the license plate and shaken shomeisho from the car are to be turned in at the front desk in the main (central) building.
Unless you are doing this in March (in which case, you'd have no refund coming anyway), you will receive a prorated refund of the yearly car tax beginning in the month following the month in which you "haisha" your car. Two or three months later, you will receive a form telling how much you have coming back. In order to get your money, however, you have to take the form to your bank. If you "haisha" your car in April or May, before you've paid for the next year's (figured from April 1 - March 31), then you'll still be liable for one or two month's worth of tax.
If you are leaving the country prior to when you'd be receiving you're refund and won't have a Japanese bank account to send it too, then you have to go to the Ibaraki Prefectural Tax Office in Tsuchiura (located on Route 125 just east of the Route 6 bypass) to get a form designating who you want the money (voucher) sent to. Whoever you designate can later send you the money.
One more point to remember if you are selling your car to an individual ­p;­p; particularly a foreigner who is only in Japan temporarily. Make sure that the buyer completes the process of transfer of name. Until that is completed, you are still liable for the yearly tax when it is due. A few years ago, one foreigner who bought a car from another foreigner never bothered to complete the change in registration. When he left the country some time later, he left the car at a junk yard (not even completing the "haisha" process). The original owner kept receiving tax bills, and it was quite a hassle getting it all straightened out. So, in this case, it is "seller beware!"
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