Soil $CO_2$ efflux can vary markedly in magnitude over both time and space, and understanding this variation is crucial for the correct measurement of $CO_2$ efflux in ecological studies. Although considerable research has quantified temporal variability in this flux, comparatively little effort has focused on its spatial variability. To account for spatial heterogeneity, we must be able to determine the number of sampling points required to adequately estimate soil $CO_2$ efflux in a target ecosystem. In this paper, we report the results of a study of the number of sampling points required for estimating soil $CO_2$ efflux using a closed-dynamic chamber in young and old Japanese cedar plantations in central Japan. The spatial heterogeneity in soil $CO_2$ efflux was significantly higher in the mature plantation than in the young stand. In the young plantation, 95% of samples of 9 randomly-chosen flux measurements from a population of 16 measurements made using 72-$cm^2$ chambers produced flux estimates within 20% of the full-population mean. In the mature plantation, 20 sampling points are required to achieve means within $pm$ 20% of the full-population mean (15 measurements) for 95% of the sample dates. Variation in soil temperature and moisture could not explain the observed spatial variation in soil $CO_2$ efflux, even though both parameters are a good predictor of temporal variation in $CO_2$ efflux. Our results and those of previous studies suggest that, on average, approximately 46 sampling points are required to estimate the mean and variance of soil $CO_2$ flux in temperate and boreal forests to a precision of $pm$ 10% at the 95% confidence level, and 12 points are required to achieve a precision of $pm$ 20%.