High penetration of distributed generation units in microgrids has caused severe frequency stability challenges. Coordinated secondary control can resolve this problem by judiciously dispatching active power resources using the communication infrastructure that supports the microgrid operations. In this paper, a distributed secondary control design for isolated microgrids is developed, and the effects of malicious attacks on the communication links are also investigated. The proposed design architecture consists of the local droop control in the primary level and a distributed dual-ascent based update in the secondary level. The objective of the latter is to achieve proportional power sharing while maintaining the system nominal frequency. Two types of malicious attacks on the distributed secondary control, namely, the link and node attacks, are investigated. To mitigate these attacks, detection and localization strategies are developed by checking the values of the dual-ascent update iterates. Numerical simulations on an isolated microgrid have been performed to demonstrate the effectiveness of the proposed control design and countermeasures against malicious attacks.