In a comparison of the German society's official indirect method and the direct LC-MS method to determine the levels of glycidol fatty acid esters (GEs) in edible oils, the indirect method showed lower GE levels in cases of a high level of GEs and/or containing partial acylglycerols (PGs). The present study used kinetic analysis to compare the scope of both methods. A kinetic model combination of reversible decomposition of GEs and 3-monochloro-1,2-propanediol forming substances (MCPD-FS) generated from PGs accurately predicted a persistent level of underestimation of commercial vegetable oils when the indirect method was used. The results of the kinetic prediction showed that the underestimation in the indirect method was proportional to the PG and GE levels in oils. Although most conventional cooking oils are low in GEs and PGs, significant error may occur in oils such as palm oil, which are reported to have a higher content of GEs and DAGs. The direct method was affected by neither the GEs nor the PGs, and proved to be a truer and more accurate determinant of GE levels in a wide range of edible oil products.