Only four refugees were accepted in the first half of 2016, when fresh asylum applications totaled 5,011, the Justice Ministry said.
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The Human Rights Watch in January described Japan's record on asylum seekers as "abysmal".
Unlike other industrialized nations, which have accepted or even encouraged immigration to refresh their labour force, Japan has remained unwelcoming, even though its shrinking, aging population is a key reason behind the economy's slow growth.
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Supporters of Japan's tough asylum process argue that the small number accepted is a consequence of a surge in bogus applications due to changes made to rules in 2010 allowing applicants to work after six months until a decision is made on their claims.
"There appears to have been an increase in the number of people who are abusing the refugee status process," said Yasuhiro Hishida, an official who reviews applications at the Justice Ministry.
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