More than 1,400 schools and nurseries will be tested over two days amid anxiety among parents over leaks at the Fukushima Daiichi nuclear plant.
The plant was crippled by last month's earthquake and tsunami.
Officials say there should be no risk to children if they keep outside a 30km (19mile) exclusion zone.
"A lot of parents are very concerned and at the local authority offices we've been flooded by queries, so we are collecting data that is objective and easy to understand, in the hope that this will allay some of those concerns," said Hiroyuki Aratake of the Fukushima Disaster Emergency Centre.
Meanwhile, workers at the nuclear plant are continuing to discharge water with low levels of contamination into the sea to free up room to store more highly radioactive water leaking at the site. (read more)