Medical Controlled Substances Transportation Act of 2011 - Amends the Controlled Substances Act to authorize a physician registered to dispense, or conduct research with, schedule II, III, IV, or V controlled substances to enter into an agreement with the Attorney General that authorizes the physician to transport controlled substances from a practice setting to another practice setting or to a disaster area and that requires the physician to: (1) notify the Attorney General in advance of any such transport; (2) identify the controlled substances to be transported, the areas from which and to which the substances will be transported, and the intended dates, mode, time, and duration (not to exceed 72 hours) of transport; and (3) maintain records in the physician's primary practice setting on the dispensing of any substance transported.