The paper investigates the active and reactive power flow in an autonomous wind diesel hybrid power system working with flywheel energy storage system (FESS)in the post high wind mode of operation. The power system operating mode transition from a stage involving only wind generator for meeting the power generation requirements to one which needs both wind generator and diesel generator (DG) for the same is met using a permanent magnet synchronous motor(PMSM) based flywheel energy storage system. This involves the stage where the DG changes from stalled stage to generation stage and needs a proper mechanism to meet the transient stage for meeting the active and reactive power requirements. This paper investigates the application of FESS for meeting the above stated transient stage including the analysis of active and reactive power flow, both from the source and to the load /sink. The wind generator described in the paper is of asynchronous type and the diesel generator is a synchronous salient pole machine. The mathematical analyses of power generating modules are discussed and the system power balance is validated using Matlab /Simulink environment. © 2017 Praise Worthy Prize S.r.l. - All rights reserved.