The J-PARC KOTO experiment searches for the rare kaon decay $K_{L}\rightarrow\pi^{0}\nu\bar\nu$. The CsI calorimeter is to measure two photons from $\pi^{0}$ in the final state, and the CsI crystals are read out from the rear end with photomultiplier tubes (PMTs). Background neutrons can be discriminated from photons by comparing the shower depth in the calorimeter. To measure the depth through the arrival-time difference between the front and rear ends, 4096 multi pixel photon counters (MPPCs) will be put on the front surface of the calorimeter. This new readout system using MPPCs is reported in this paper.