Farmland reallocation between farmers through rental transactions is critical for improving Japanese rice productivity. This study examined effects of socio-institutional and emotional factors as well as economic factors on rental transactions. A stochastic choice model was applied to contingent valuation data by considering regional heteroscedasticity. Empirical results showed (1) existence of economic inefficiencies, 3% loss of economic surplus due to socio-institutional restriction, which is probably reflected in transaction costs; (2) a 15% reduction in surplus due to emotional reluctance of farmers; and (3) strong influences of rice price, wages, and geographical location on the rental rate and agreement level.