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We study the problem of efficient data aggregation in unreliable wireless sensor networks by designing a fault tolerant data aggregation protocol. A fault tolerant data aggregation protocol consists of two parts: basic aggregation scheduling and amendment strategies. On default, data is aggregated according to the basic aggregation scheduling strategy. The amendment strategy will start automatically when a middle sensor node is out of service. We focus our attention on the amendment strategies and assume that the network adopts a connected dominating set (CDS) based aggregation scheduling as its basic aggregation scheduling strategy. The amendment scheme includes localized aggregation tree repairing algorithms and distributed rescheduling algorithms. The former are used to find a new aggregation tree for every child of the corrupted node, whereas the latter are used to achieve interference free data aggregation scheduling after the amendment. These amendment strategies impact only a very limited number of nodes near the corrupted node and the amendment process is transparent to all the other nodes. Theoretical analyses and simulations show that the scheme greatly improves the efficiency of the data aggregation operation by reducing both message and time costs compared to rebuilding the aggregation tree and rescheduling the entire network.