A system and method for protocol independent multi-flow table routing includes a first flow table, a second flow table, and a shared hash table accessible by both the first flow table and the second flow table. Upon receipt of a packet, a first secure signature of a first lookup key is generated for the first flow table, and a second secure signature of a second lookup key is generated for the second flow table. The shared hash table stores both the first secure signature in association with a first value corresponding to the first secure signature, and the second secure signature along with a second value corresponding to the second secure signature. The first and second values indicate destination information for the packet.