Is the tax incentive system beneficial to the policy's intended beneficiary, or other economic agents? To clarify this issue, this paper examines the impact of Japan's taxation system on housing prices using the first-time homebuyer credit as an example. The concept used here is implicit taxes generated by the purchase of tax-preferred assets. Moreover, the asset price is increased by the amount of the implicit taxes when compared to the case without the preferential taxation system. Based on this concept, the analysis shows that property prices with a preferential taxation system are higher than those without. The estimated implicit taxes amount accounts for a large portion of the maximum amount of special tax credits available to homebuyers, implying that the program’s benefits are likely to accrue to home sellers rather than homebuyers. This is an important finding that should be considered when discussing housing taxation in the future.