A question about the education status of children in the 2010 census was left blank for about 13,000 foreign children, according to Kyodo News analysis of the data.
The rate of "not known" — 16 percent of foreign children aged 7 to 14 — compares with just 0.01 percent for Japanese children in the same age group.
Possible responses included the child "Is attending," "Will attend" or "Graduated from" school. Leaving the section blank was categorized as "not known," according to the census division of the Internal Affairs and Communications Ministry.
It is unclear if people left it blank because they did not understand the question or wanted to avoid declaring that their children are not in school, but 39.5 percent of the people who did not answer also failed to fill in the section asking about their nationality.
Among declared nationalities, 15.9 percent of "not knowns" were Peruvians, 14.9 percent Vietnamese and 14.6 percent Chinese.
Some did declare a not-in-school status. About 430 foreign children from 7 to 14 years old, or 0.55 percent, were shown as not attending school, according to the analysis.
The government carries out the census every five years on Japanese and foreign residents in the country.
Questions about education are made every 10 years.