The tests, designed to spot early symptoms of thyroid cancer, will be conducted every two years until the age of 20 and then every five years, according to Japanese news reports.
An estimated 360,000 young residents will be entitled to the free medical tests, which will start operating from October this year, with further in-depth urine and blood testing taking places if any abnormalities are discovered.
News of the lifelong testing follows growing concern surrounding the potential health impact of the still stricken Fukushima nuclear power plant on residents in surrounding regions.
Following the March 11 earthquake and tsunami, the power plant has leaked radiation into the surrounding soil, air and sea, prompting evacuation of the immediate area and a string of food scares relating to local produce.
Nearly 3,000 cattle feared to have been contaminated with radioactive caesium have been shipped nationwide and are suspected of being sold to supermarkets and restaurants across the country.
Tokyo Electric Power Company, operators of the damaged power plant, are expected to face picking up the bill for the new plan to buy and burn all tainted beef, with estimated costs expected to run to £15.7 million (two billion yen).
The authorities in Fukushima also this week mobilised close to 4,000 people – mostly residents – to help clean up areas to speed up the decontamination process across the region.
Thousands of residents are helping to haul mud and debris from streets and gutters as well as weeding in a bid to assist with the clean up process in areas where high radiation levels have been recorded.
By Danielle Demetriou in Tokyo