We simultaneously measured radon and thoron exhalation rates in areas of weathered acid rocks in Japan to investigate the relationship between them and between measured and calculated radon exhalation rates. To calculate the radon exhalation rate, we used an equation proposed by UNSCEAR. Our analysis showed that both the radon and thoron exhalation rates measured at one location in a natural environment fluctuated widely, even within one day. We found a strong correlation between the radon and thoron exhalation rates. The measured radon exhalation rates tended to be lower than the calculated values: the mean ratio of the measured exhalation rate to the calculated rate was 0.65. We concluded that the UNSCEAR equation is applicable under a controlled environment (temperature, humidity, etc.), but not where there are artificial underground structures that may influence the transportation of radon in soil.