Migratory Bird Protection Act of 2021 This bill prohibits the incidental taking (e.g., capturing or killing) of migratory birds by commercial activities unless the activity is authorized under a permit or is identified as posing de minimis risk to migratory birds. The U.S. Fish and Wildlife Service (USFWS) must regulate such incidental taking, including by (1) issuing general permits for certain industries, (2) creating a mitigation fee for any incidental taking of migratory birds, and (3) identifying categories of de minimis risk activities that are exempt from liability for the taking of migratory birds. In addition, the USFWS must establish and maintain a research program (1) to evaluate the impacts of commercial activities on birds, (2) to evaluate the effectiveness of best management practices and technologies to avoid or minimize such impacts, and (3) to develop new or improved best management practices and technologies.