The perturbations of the ionosphere which are observed prior to significant earthquakes (EQs) have long been investigated and could be considered promising for short-term EQ prediction. One way to monitor ionospheric perturbations is by studying VLF/LF electromagnetic wave propagation through the lower ionosphere between specific transmitters and receivers. For this purpose, a network of eight receivers has been deployed throughout Japan which receive subionospheric signals from different transmitters located both in the same and other countries. In this study we analyze, in terms of the recently proposed natural time analysis, the data recorded by the above-mentioned network prior to the catastrophic 2016 Kumamoto fault-type EQs, which were as huge as the former 1995 Kobe EQ. These EQs occurred within a two-day period (14 April: and , 15 April: ) at shallow depths (~10 km), while their epicenters were adjacent. Our results show that lower ionospheric perturbations present critical dynamics from two weeks up to two days before the main shock occurrence. The results are compared to those by the conventional nighttime fluctuation method obtained for the same dataset and exhibit consistency. Finally, the temporal evolutions of criticality in ionospheric parameters and those in the lithosphere as seen from the ULF electromagnetic emissions are discussed in the context of the lithosphere-atmosphere-ionosphere coupling.