Despite positive political developments for Ainu in 2008, members of the indigenous community still faced major obstacles in 2009, according to survey results released in June 2009 by the Hokkaido University Centre for Ainu and Indigenous Studies. The study indicated that household incomes among Japan's 50,000 Ainu are only 60 per cent of the national average, and college advancement rates are half those of other Japanese people. The chief of the University Centre told media that such data could be useful to the government in formulating policies in support of Ainu.

In 2008, the Japanese House of Representatives officially classified the Ainu as an 'indigenous people'. Many commentators saw this as a substantial step forward, as the resolution was linked to the UN Declaration on the Rights of Indigenous Peoples (UNDRIP). The government set up an expert panel to determine future policies to uphold Ainu rights and help guide policy. The Hokkaido University June 2009 report suggested that the government has a long way to go to make up for past injustices, which include the seizure of traditional lands, cultural repression and forced assimilation, including a prohibition on use of the Ainu language. More than half the survey respondents said they had no experience of preserving aspects of their culture, such as their language, song, dance and storytelling. Less than 70 per cent of Ainu youth make it to high school, 10 per cent of those drop out. In universities and colleges, the drop-out rate is 19 per cent. More than half the respondents said they expected government to enact measures to help them access education. The panel established in 2008 submitted a report to the Japanese government in June 2009, which stated that the government bears a 'strong responsibility' for restoring Ainu culture. Included in the recommendations was legislation that would give Ainu special access to land and water resources so that they could maintain such traditions as salmon-fishing. According to a 30 July 2009 article in the Japan Times, the government plans to establish a consultative body on Ainu affairs, which will include Ainu representatives.

Prejudice against Burakumin remains widespread. Ethnically non-distinct from the majority of Japanese, they were the lowest caste during the Edo period from 1603 to 1868. Although the caste system has long since been abolished, discrimination remains and the issue was brought to the forefront in 2009 when Google posted a map online that distinguished 'burakus', or districts where many descendants of Burakumin still live. The Japan Times quoted sources saying that descendants of burakumin are often blacklisted from jobs and face other forms of discrimination. In a July 2009 report, Freedom House also noted, 'Japan's three million burakumin, who are descendents of feudal era outcasts, and the indigenous Ainu minority still suffer from entrenched societal discrimination that prevents them from gaining equal access to housing and employment opportunities.' During its 23 July 2009 review of Japan's report to the UN Committee on the Elimination of Discrimination against Women, the Committee, 'expressed regret at the lack of information and statistics concerning minority women'. In a report released by the UN, the committee also noted a lack of 'any proactive measures, such as a policy framework to promote their rights'.

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