Mobile agent (MA)-based wireless sensor networks present a good alternative to the traditional client/server paradigm. Instead of sending the data gathered by each node to the sink as in client/server, MAs migrate to the sensor nodes (SNs) to collect data, thus reducing energy consumption and bandwidth usage. For MAs, to migrate among SNs, an itinerary should be planned before the migration. Many approaches have been proposed to solve the problem of itinerary planning for MAs, but all of these approaches are based on the assumption that MAs visit all SNs. This assumption, however, is inefficient because of the increasing size of the MAs after visiting each node. Also, in case of node(s) failure, as it is often the case in WSNs, the MAs may not be able to migrate among SNs. None of the proposed approaches takes into consideration the problem of fault tolerance. In this paper, we propose multi-mobile agent itinerary planning-based energy and fault aware data aggregation in wireless sensor networks (MAEF) to plan itineraries for MAs. This can be achieved by grouping nodes in clusters and planning itineraries efficiently among cluster heads (CHs) only. What is more, an alternative itinerary is planned in case of node(s) failure. The simulation result clearly shows that our novel approach performs better than the existing ones.