Thousands of refugees are still making their way through the Balkans toward Germany. Source: AFP/File
The country has long been nervous about an influx of refugees into its homogeneous society and has tightly restricted the number it accepts.
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Of the thousands seeking refugee status, five were Syrian, only three of which were accepted -- a far cry from the massive influx of Syrians into Europe from the war-torn Middle East nation last year.
The justice ministry said it received a record 7,586 refugee applications in 2015, meaning more than 99 per cent of requests were rejected.
Other accepted applicants included six from Afghanistan, three Ethiopians and three Sri Lankans.
The ministry said number of refugees accepted last year was a jump from 11 in 2014 and six in 2013.
The Japan Association for Refugees said despite the progress in recent years, more applicants should be accepted.
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"We hope that (Japan) will hold discussions with UNHCR and NGOs and swiftly consider measures to certify refugees in line with international standards," the association said.
Human rights activists, lawyers and migrant communities in Japan have complained for years about harsh treatment by immigration officials and about conditions at detention centres.
The UN refugee agency says Japan is home to 2,419 refugees, compared to its Group of Seven ally the United States with 267,222 and Turkey, which has 1.8 million refugees.
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