According to the latest NIID report, 35,960 cases were reported from about 3,000 monitoring medical institutions nationwide during the week leading up to July 7, Xinhua news agency reported.
An average of 11.46 cases per medical institution was reported during the reporting week, remaining above the warning level of five cases per institution in 38 prefectures.
During the reported period, the central Japanese prefecture of Mie recorded the highest number of cases per institution at 25.98, followed by Saitama with 18.8.
HFMD, a viral infection causing blister-like rashes on the hands, feet, and inside the mouth, primarily affects children under the age of five, who account for about 90 per cent of cases.
Symptoms include fever, loss of appetite, feeling unwell, skin rashes and sore throat. Mouth sores and ulcers on the tongue, gums and the inside of the cheeks can also indicate HFMD infection.
Japan's health ministry is urging increased hygiene measures to curb the spread of the disease.
A health ministry official advised the public to wash hands with soap and avoid sharing towels, adding that alcohol-based disinfectants are less effective against HFMD, which typically spreads during the summer.
