In automated manufacturing systems (AMSs), because of unpredictable failures, resources can lose functions such that the deadlock control methods, in existence, are invalidated. In this paper, a robust deadlock control approach is proposed for AMSs with multiple unreliable resources. The considered AMSs modelled by Petri nets (PNs) allow to acquire different types of resources at each processing stage. In order to visualise the fact that resource failures occur in AMSs, recovery subnets are designed for the modelling AMSs to depict the failures and recoveries of resources. Based on a siphon detection method performed by a set of integer linear programming formulations, a control specification is proposed. Control places (monitors) with their control variables are designed for the detected unmarked siphons at a marking to guarantee that they are always marked even if some unreliable resources break down. Iteratively, all unmarked siphons are detected and controlled. Therefore, a robust deadlock supervisor is synthesised to ensure the controlled system's liveness no matter there exist resource failures or not. The theoretical analyses and proof are given to verify the correctness of the proposed method. Finally, the comparative studies are presented to expound the proposed method's effectiveness and efficiency.