Turkmenistan's minority groups include the Kazakh, Russian and Uzbek minorities, as well as the ethnic Baluch community, which CERD has drawn particular attention to as being at risk of forced assimilation. Human rights organizations have also reported children from ethnic minorities being denied the opportunity to study in their own languages due to the steady closure of schools and reduced resources. Some minorities also struggle to secure formal legal recognition despite being based long-term in the country, creating further difficulties for them when accessing public services and other rights.

In September 2014, a local human rights organization reported on the plight of several thousand ethnic Uzbeks, mainly in the eastern provinces, who for over 20 years had failed to obtain passports and become full citizens of their own country. Almost 10,000 people from Dashoguz and Lebap provinces have reportedly requested citizenship without success. Many had studied in Uzbekistan and graduated there after the Soviet Union collapsed in 1991, during the period when national passports were being issued in Turkmenistan. When they returned, their Soviet passports were no longer considered valid. The organization reported that their children and grandchildren had also not been able to obtain Turkmen passports. Meanwhile, several women from Uzbekistan who had married men from Turkmenistan and moved to the country had reportedly been deported, thus breaking up families. Those without internal passports have reportedly been deprived of opportunities to find official employment, leave the country or move to the capital to earn money.

Human rights activists have estimated that about 100,000 Turkmenistan nationals of both Russian and Turkmen ethnicity also hold Russian passports, under a 1993 bilateral Agreement on Dual Citizenship. However, in autumn 2013 the State Migration Service of Turkmenistan stopped issuing new passports to dual nationals. As a result it has become impossible for them to leave the country. In May 2014, Turkmenistan officially informed the Russian Foreign Ministry that it would terminate the Agreement on 18 May 2015.

In June 2014, Amnesty International published an appeal urging the Turkmen authorities to grant a retrial to Mansur Mingelov, a Baluchi human rights activist who began a hunger strike on 19 May to protest a sentence widely condemned as unfair. Mingelov had been arrested in 2012 and convicted to 22 years in prison for alleged drug and child pornography offences after documenting evidence of police torture against ethnic Baluch. Being in a critical condition, he reportedly ended his hunger strike on 8 June after a number of Turkmen officials visited him in the Seidi labour camp, and his treatment improved. The day the appeal was published, the president issued a statement highlighting the importance of upholding the rule of law and subjecting each criminal accusation to a thorough review.

Turkmenistan, a largely Sunni Muslim country, has long been intolerant towards its religious minorities, including Protestants and Jehovah's Witnesses as well as Shi'a Muslims. In 2014, the US State Department added Turkmenistan to its list of 'worst religious freedom violators'. Ethnic Turkmen converts to Protestantism and other Christian denominations are reportedly even more likely to be exposed to harassment from the state than those from minority ethnic groups. Some have been arrested for their beliefs, though in October eight prisoners of conscience jailed for exercising freedom of religion or belief were released from their incarceration in a labour camp under presidential amnesty. Six were conscientious objectors to military service, while the other two had been falsely convicted as punishment for their beliefs.

While access to information is in many ways strictly controlled in Turkmenistan, Russian-speaking urban residents are able to watch news channels broadcast from Russia via satellite television. The government has reportedly appeared uncomfortable about coverage of the 2014 events in Ukraine, and in April it was reported that access to the broadcasts was affected by more interference, poor signals and in some cases blackouts. Like other Central Asian countries, Turkmenistan had a large influx of Russians and other European ethnicities to its urban areas during the Russian Empire and Soviet Union. Most remaining Russians and Ukrainians live in or near the capital, Ashgabat, and other urban centres. While Russians and Ukrainians constituted the largest minority group at the time of independence, their numbers decreased dramatically in the wake of independence and more recently in 2003, when Russians lost their dual citizenship rights.

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