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The KOTO experiment at J-PARC, Japan, aims to observe the rare neutral kaon decay mode KL\rightarrow \pi ^{0}\nu \bar {\nu } . After the first experimental run in May 2013 at a 24-kW beam power, the KOTO data acquisition (DAQ) system was upgraded in 2015 to provide efficient and reliable data collection at higher beam intensities. Lossless data compression in the analog-to-digital converter modules was implemented to reduce the size of data packets, resulting in a threefold increase in data collection rate. A new software trigger on a 47-node cluster was designed to use Infiniband hardware with message passing interface protocol to establish a mesh network inside the computer clusters for parallel data processing. The upgrade to the KOTO DAQ system was commissioned in 2015 and successfully collected data with a beam intensity of up to 42 kW. In preparation for increasing beam intensities in future runs, the hardware trigger upgrades using the reconfigurable clustering element platform technology are under development. [ABSTRACT FROM AUTHOR]