All religious activity remains under tight government control. The Muftiate (Muslim Board) is controlled from the inside through the state's appointment of the chief mufti and other imams, while all other faiths are controlled from the outside through intimidation, threats and arbitrary interference. All religious communities have to abide by the highly restrictive law regulating religious practice, which bans all unregistered religious activity and strictly limits registered religious expression.

Although the government allows Sunni Islam to operate (within tightly controlled limits), this is not the case for Shia Islam, which is mainly professed by the ethnic Azeri and Iranian minorities in the west of the country. Under former President Saparmurat Niyazov (who ruled for 21 years and died in 2006), a Turkmen-speaking and ethnically homogeneous Turkmen national identity was promoted, of which Sunni Islam was seen as a part. The policy continues to be evident in official harassment of ethnic Turkmen members of religious minorities, as well as of non-Turkmen minorities. Ethnic Turkmens who are members of non-Muslim faiths face public humiliation and accusations from officials of betraying their nation. And while the Russian Orthodox Church is tolerated, the Armenian Apostolic Church has been banned from being revived. An estimated 15 per cent of those who attend Russian Orthodox churches are said by local people to be Armenians. No Armenian Apostolic communities have legal status.

Acquiring new places of worship is almost impossible for religious communities. While the Russian Orthodox Church, perhaps the least restricted faith, was finally able to consecrate three new churches in 2009 after long official obstruction, other communities without existing places of worship are confined to ad hoc arrangements to which the authorities can object at any point. No official compensation has been given for the many mosques, the Hare Krishna temple and the Seventh-day Adventist church bulldozed, or for Protestant churches confiscated in the last decade. All the mosques which have been built in recent years have been by decision of the government and often with government funds, despite the constitutional separation of religion from the state. No independent mosques are allowed to open or function.

Religious believers – especially Protestants and Jehovah's Witnesses – have been fired from their jobs or evicted from their homes because of their faith. Their children have also been threatened with expulsion from schools, including in 2009.

Religious communities are forcibly isolated from their fellow-believers abroad. Many known active religious believers are blacklisted from leaving the country, even if they have a valid passport. Rarely do officials give reasons why individuals are entered in the computer travel blacklist. Those barred from travelling at Ashgabad airport receive no compensation for their wasted airplane tickets. In previous years, the government allowed only 188 Muslim pilgrims to travel each year on the hajj pilgrimage to Mecca, but in 2009 it banned any from travelling, citing fears of the spread of the H1N1 virus. Turkmenistan's hajj quota is believed to be about 5,000. Only in exceptional circumstances does the government's Religious Affairs Committee allow religious communities to invite fellow-believers from abroad.

No alternative to compulsory military service is offered, and Jehovah's Witnesses have in recent years borne the brunt of this. Speaking at the Human Rights Council (HRC) in Geneva in March 2009, the head of the Turkmen government delegation Shirin Akhmedova rejected the recommendations from numerous international organizations and oversight mechanisms – including the UN Special Rapporteur on freedom of religion and belief, Asma Jahangir – that Turkmenistan introduce a civilian alternative to compulsory military service. While in 2007 and 2008 most conscientious objectors were given suspended sentences, living at home with many restrictions and often having to hand over some of their earnings to the state, the policy of imprisoning conscientious objectors resumed in May 2009.

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