The commercial asset value of sequestered forest carbon is based on protocols employed globally, however, their scientific basis has not been validated. We review and analyze commercial forest carbon protocols and offsets, claimed to have reduced net greenhouse gas emissions, issued by the California Air Resources Board and validated by the Climate Action Reserve (CARB-CAR). CARB-CAR protocol annual offsets, resulting from forest mensuration and growth simulation models, are compared with a population of forest field sites for which annual net ecosystem exchange (NEE) of carbon was measured directly as flux by CO2 eddy covariance, a meteorologically based method integrating forest carbon pools. We characterize differences between the protocols by testing the null hypothesis that the CARB-CAR commercial annual offset data fall within the boundaries of directly measured forest carbon NEE; gC m-2yr-1 are compared for both datasets. Irrespective of geographic location and project type, the CARB-CAR population annual mean value is significantly different from the NEE population mean at the 95% confidence interval, rejecting the null hypothesis. The CARB-CAR population exhibits standard deviation ~5x that of the NEE natural ranges; the variance exceeds the 5% compliance limit for invalidation of CARB-CAR offsets. Exclusion of the soil carbon pool typical for CARB-CAR net carbon budgets pose insuperable carbon accounting uncertainty for offsets that extend to vendor platforms and policies including the United Nations Program on Reducing Emissions from Deforestation and Forest Degradation and the Paris Agreement. NEE methodology for commercial forest carbon offsets ensures in situ molecular specificity, verification of claims for net carbon balance, performance-based pricing and harmonization of carbon protocols for voluntary and compliance markets worldwide, in contrast to continuing uncertainty posed by traditional estimation-based forest carbon protocols.