Industrial agriculture is only more efficient than sustainable or traditional agriculture in narrow calculations which leave out environmental and social costs. Classical yield comparisons narrowly focus on crop output per unit area, assuming that large areas are cropped with the same produce, which is not the case for small-scale and sustainable agriculture. A single measure of yield is not adequate either to measure productivity, because in industrial agriculture yields decline over time due to loss of soil fertility (or they remain stable but with added input costs), while they remain stable or increase with sustainable agriculture. Also, energy efficiency in production is neglected in the classical yield comparisons (sustainable agriculture is much more energy efficient than industrial agriculture).
McAfee, K. (2006) Sustainability and Social Justice in the Global Food System: Contributions from the Yale workshop. In Pimbert, M, (Ed.) Agroecology and the Stuglle for Food Soveregnity in the Americas. London. IIED.