This paper addresses the design and implementation of distributed control structures for Modular Power Electronic Transformers (PETs). Medium voltage modular PETs are characterized by a large count of controlled power devices (easily in the range of hundreds or even thousands) and strict isolation requirements, both between modules in the high-voltage side and between the primary and secondary sides of each module as well. Due to this, distributed control structures have significant advantages compared to centralized ones. However, design of the distributed control structure is not trivial. Energization and start-up of the PET, as well as the required reconfigurations in the event of a module failure, to maintain the PET operative, can be especially challenging in this case. This paper discusses potential flexible, fault tolerant distributed control structures for modular PETs. Performance of the proposed solutions is verified experimentally.