Amid clamour for an effective way to punish a Pyongyang leadership that has proved immune to years of diplomatic pressure, youngsters who have never lived under the regime are bearing the brunt of Japanese anger.
The schools many of these children attend are having their funding withdrawn by Japan, leaving students and parents wondering why they are being punished for something they cannot control.
"Every time something happens in our fatherland of Korea, small Korean children get harassed verbally and physically by those who watch the news," said Kim Su-Hong, a 17-year-old pupil at a school in Yokohama, near Tokyo.
"The daily reality of discrimination that we face really hurts."
There are around 500,000 ethnic Koreans in Japan, mostly descendants of migrants and forced workers from Tokyo's sometimes brutal 1910-1945 occupation of the Korean peninsula.
Many are effectively stateless, having forfeited their Japanese nationality with Japan's 1945 defeat. They remain without the vote in their host country.
When Korea was divided in 1953, they were forced to choose between allegiance to the US-allied Seoul or to Beijing-backed Pyongyang.
Many felt the new government in the South had abandoned Koreans in Japan and gravitated towards institutions generously funded by Kim Il-Sung's North, who lavished money on the community for the establishment and running of dozens of schools.
Since 1957, a total of 48 billion yen ($511 million) has been sent from the communist state, supporting some 70 ethnic Korean schools throughout Japan, according to an official of the General Association of Korean Residents in Japan (Chongryon), the North's de facto embassy.
The schools proudly display portraits of Kim Il-Sung and Kim Jong-Il in their classrooms, which many parents and teachers say represents their gratefulness for the leaders' support.
Until recently, these schools -- to which Japanese people are free to send their children -- received the same local government support as any other foreign school in Japan.
But patience was tested after Pyongyang fired a rocket over Okinawa last year, in what it said was a satellite launch, but the US and its allies said was a poorly-disguised ballistic missile test.
Then, after the February 12 underground nuclear explosion, the local government in Kanagawa prefecture decided it would halt its 60 million yen annual subsidy to the five schools in its area.
Governor Yuji Kuroiwa announced that after 35 years of helping to prop up the schools he could no longer justify the spending of taxpayers' money.
"North Korea fired its missile and went ahead with a nuclear test. They are such provocative actions against the wishes of the international community," he said at a press conference.
"I have no intention of continuing to defend Korean schools anymore."
The decision is a major blow to the schools, which campaigned long and hard for the right to receive the local government cash.
However, sympathy among Japanese for ethnic Koreans is in short supply.
In 2002, Pyongyang admitted what Japan had long suspected -- that North Korean agents kidnapped Japanese in the 1970s and 1980s to train their spies in Japanese language and culture.
Then-leader Kim Jong-Il later allowed five of them and their families to return to Japan, but many in the country believe Kim did not come clean and say other abductees remain unaccounted for.
Chang Mal-Ryo, a teacher at the Yokohama Korean school, said the schools were built by the generations who came from the Korean peninsula before it was divided along the 38th parallel and should be free from the effects of geopolitics.
She said the withdrawal of Japanese funding would do nothing to help the ethnic Koreans wean themselves off North Korean support.
"I once thought maybe the schools could become independent (from Pyongyang)
-- but not now," she said. "Not until Japan becomes completely free of discrimination against Koreans."
And beyond all the politicking, Han Bok-Myong, a mother of three students at the school, says it is the children who are suffering.
"We all know, and children all know, that abductions and nuclear tests should never occur," she said.
"But these issues should never be the reason to take away the children's right to an education."