A method for controlling a malfunction catalyst diagnostic test that determines a malfunction status of a catalyst within a selective catalytic reduction device includes monitoring an exhaust gas flow within an aftertreatment system, estimating an effect of the exhaust gas flow on an estimated reductant storage on a catalyst within the selective catalytic reduction device, and selectively disabling the malfunction catalyst diagnostic test based upon the estimating the effect of the exhaust gas flow on the estimated reductant storage.