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The estimation of output supply and inputs demand in farming sector with the assumption of full economic efficiency may result in false policy decisions. This article investigates the effects of irrigated wheat economic inefficiency on output supply and inputs demand in the period 2001-2009. After estimating the economic inefficiency by the use of production and cost stochastic models, the output supply and inputs demand of irrigated wheat are obtained through seemingly unrelated regression method. Results show that technical, allocative and economic inefficiency in irrigated wheat production in Iran are 21, 23 and 38 percent respectively. Moreover, the slope of output supply function is strongly affected by the related economic inefficiency in profit function and inefficiency changes input’s demand coefficients. Results also show that technical inefficiency has a greater effect on inputs demand compared to the allocative inefficiency.