The presiding judge at the Supreme Court rejected the suit filed by 387 people who were within 12 kilometres (7.5 miles) of ground zero when the attack happened in August 1945, but outside the affected zone recognised by the government, according to public broadcaster NHK and a court spokesman.
Those within 12 kilometres of ground zero but outside the designated zone can receive free treatment only for mental illness associated with the bombing and complications caused by mental illness, according to a Nagasaki prefectural official.
There are a total of 6,278 people in this category, he said.
They have to live in Nagasaki to be able to receive free medical treatment.
"Officially recognised survivors, on the other hand, can receive free treatment for almost all kinds of diseases no matter where they live," the official told AFP.
"I don't know how to explain to those who are struggling to pay medical fees and those who are hospitalised," she said.
The Japanese government defines the officially recognised affected area as an oval shape seven kilometres wide and 12 kilometres long.
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