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Deadlock prevention is a crucial step in the modeling of flexible manufacturing systems. In the Petri net framework, deadlock prevention policies based on siphon control are often employed, since it is easy to specify generalized mutual exclusion constraints that avoid the emptying of siphons. However, such policies may require an excessive computational load and result in impractical oversized control subnets. This is often a consequence of the redundancy in the control conditions derived from siphons. In this paper, a novel method is proposed that provides small size controllers, based on a set covering approach that conveniently relates siphons and markings. Some examples are provided to demonstrate the feasibility of the approach and to compare it with other methods proposed in the literature.