This paper presents a fault-tolerant secondary and adaptive primary microgrid control scheme using a hybrid multi-agent system (MAS), capable of operating either in a semi-centralised or distributed manner. The proposed scheme includes a droop-based primary level that considers the microgrid energy reserves in production and storage. The secondary level is responsible for: a) the microgrid units' coordination, b) voltage and frequency restoration and c) calculation of the droop/ reversed-droop coefficients. The suggested architecture is arranged upon a group of dedicated asset agents that collect local measurements, take decisions independently and, collaborate in order to achieve more complex control objectives. Additionally, a supervising agent is added to fulfill secondary level objectives. The hybrid MAS can operate either with or without the supervising agent operational, manifesting fast redistribution of the supervising agent tasks. The proposed hybrid scheme is tested in simulation upon two separate physical microgrids using three scenarios. Additionally, a comparison with conventional control methodologies is performed in order to illustrate further the operation of a hybrid approach. Overall, results show that the proposed control framework exhibits unique characteristics regarding reconfigurability and fault-tolerance, while power quality and improved load sharing are ensured even in case of critical component failure.