Monitoring nutritional status of the population is essential in the development and evaluation of national or local health policies. In this study, we aimed to demonstrate analysis on the trends in dietary intake of energy and macronutrients, as well as Na, in Japanese population using the data of series of cross-sectional national surveys – the National Nutrition Survey (NNS) and the National Health Nutrition Survey (NHNS) – during the period from 1995 to 2016. The NNS and NHNS participants aged 20–79 years were included in the analysis. Dietary intake was estimated using 1-d household-based dietary record. The trend in total energy intake, energy intake from macronutrients (fat and protein), Na intake and energy-adjusted Na intake were analysed using regression models adjusted to 2010 age distribution and anthropometry status. A total of 94 270 men and 107 890 women were included the analysis. Total energy intake showed a decreasing trend in both men and women. Similarly, energy intake from protein decreased, but energy intake (%) from fat increased in both sexes. Energy-adjusted Na intake showed a decreasing trend in both men and women. This study identified the decrease in total energy intake and energy intake from protein, whereas there were inverse trends in energy intake from fat among Japanese adults. Continued monitoring of trends in dietary intake will be needed, and there should be efforts to increase the accuracy of current survey procedures.