About 150,000 people with intractable diseases lost their financial support at the start of this year after a Japanese government program was revised.
The health ministry released the figures on Wednesday.
When the government revised its support system in 2015, the number of diseases covered by the subsidies was increased from 56 to 331. But patients with relatively less serious conditions do not receive any support unless their medical costs exceed a certain amount.
The new support system was applied in January 2018 after a 3-year transition period.
The ministry says 720,000 were subject to the interim measures, and about 20 percent of them lost their coverage at the end of the grace period.
Over 80,000 had their applications for support turned down, while more than 60,000 did not apply.
The ministry says it will carry out a survey of patients with intractable diseases to assess the impact of the revised system on their lives.