Energy conservation and network throughput are the important performance metrics for wireless sensor network applications because the network may prefer to deploy in an unattended and unmanned geographical environment. The wireless sensor nodes are having irreplaceable and limited power source hence the performance of WSN is purely depends on lifetime of each sensor node. The node energy exhaust happens quick when continuous sensing, processing, storing, and communication of the parameters of targeted environment. Cluster topology is an important technique proposed to achieve energy conservation and better network lifetime. The existing clustering techniques are not capable to achieve higher throughput and desired network lifetime due to un-coverage area in sensor field. Hence, we proposed a new energy efficient clustering with hybrid coverage mechanism (EEC-HC) to achieve energy efficiency, better coverage and high throughput. The proposed EEC-HC has estimated the minimum clustering cost function and optimum number of sensor nodes using optimum distance to minimize the un-coverage area in sensor field. The EEC-HC mechanism has given a better solution for detection of animal intrusions in agriculture fields and provided smart fencing. © 2018 Eastern Macedonia and Thrace Institute of Technology.