In the past 10 years or so, there have been growing concerns in Japan that migration trends, such as large in‐migration to the Tokyo metropolitan area (TMA) at the national scale and large movements from the suburbs to the centres at the metropolitan scale, have widened the core–periphery disparities at each scale under national population decline. However, the COVID‐19 pandemic led to unexpected changes in these migration patterns, such as a weakened population concentration in the TMA. This study aims to examine internal migration trends from 2012, on axes of core–periphery in Japan and centre–suburbs in metropolitan areas, and the changes in the migration patterns caused by the pandemic in 2020. First, we prepared intermunicipal origin–destination tables by estimating the suppressed flows in 2012–2020 using the iterative proportional fitting technique, and then we calculated the net migration and migration efficiency indices based on seven area types: centre and suburbs of the TMA, centres and suburbs of major metropolitan areas, centres and suburbs of other metropolitan areas and nonmetropolitan areas. The results indicate that the 2020 migration efficiency in the centre of the TMA drastically dropped to the lowest level during the study period, contrasting with an upward trend in 2012–2019. The pandemic strongly affected the migration patterns from/to and within the TMA, with much net gain in the suburbs from the centre, but the impact of migration efficiencies among the other areas was minimal. These findings can help in providing direction for the postpandemic policy challenge of spatial planning in Japan, for example, the weakened but still widening disparities between the TMA and the other regions and the renewed threat of urban sprawl caused by the increased migration from the centre to the suburbs within the TMA.