The Sixth Report of Fukushima Prefecture Health Management Survey, released in April, included examinations of 38,114 children, of whom 35.3 percent - some 13,460 children - were found to have cysts or nodules of up to 5 mm (0.197 inches) on their thyroids.
A further 0.5 percent, totalling 186 youngsters, had nodules larger than 5.1 mm (0.2 inches).
A study by the Japan Thyroid Association in 2001 found that zero percent of children in the city of Nagasaki had nodules and only 0.8 percent had cysts on their thyroids.
"Yes, 35.8 percent of children in the study have lumps or cysts, but this is not the same as cancer," said Naomi Takagi, an associate professor at Fukushima University Medical School Hospital, which administered the tests.
"We do not know that cause of this, but it is hard to believe that is due to the effects of radiation," she said. "This is an early test and we will only see the effects of radiation exposure after four or five years."
The local authority is carrying out long-term testing of children who were under the age of 18 on March 11 last year, the day on which the magnitude-9 Great East Japan struck off the coast of north-east Japan, triggering the massive tsunami that crippled the Fukushima nuclear plant.
Thyroid examinations were first conducted in October last year and will be carried out every two years up to the age of 20 and every five years for the rest of the children's lives.
A second report has been issued by Japan's Institute of Radiological Sciences in which it found that some children living close to the plant were exposed to "lifetime" doses of radiation to their thyroid glands.