A collimated neutron flux array system in JT-60U successfully upgraded performance of higher counting rate and the capability to detect 14 MeV neutrons as well by using a fast digitizer in 2006. Additionally, detailed analysis of the recorded waveform on JT-60U and FNS has provided us new findings. In this paper, firstly, characteristics of pulse shapes and neutron-gamma discrimination parameters investigated by the detailed analysis of digitized waveform data are described. Next, new data analysis procedure for neutron-gamma discrimination based on the characteristics is proposed. In the new procedure, an appropriate projection surface, on which we can define the discrimination boundary, has been introduced in three-dimensional discrimination parameter space. The problem of "pulse height variation", which occurs when a counting rate is high in high performance plasma, and its countermeasures are also presented. The system using the countermeasure of a booster method successfully has avoided the problem in the high neutron flux condition of ∼2 × 10 5 counts/s on FNS.