In May 2003, the Jewish community received an official letter ordering them to vacate the buildings, including the synagogue, by July of that year. Demolition, originally scheduled for 2004, began in early February 2006 with the destruction of the community's mikvah, or ritual bath, kosher butcher, and classrooms. Demolition of the synagogue was delayed until June 2008 due to international protests and a series of court actions. The synagogue was finally demolished on 22 June 2008.
At the time demolition began, the synagogue was a functioning house of worship serving the city's 150 Jews, and the last remaining synagogue in Tajikistan. The destruction of the synagogue was surrounded by controversy. The government argued that the building was of no historical significance. The Jewish community (led by Rabbi Mikhail Abdurakhmanov) stated that as the last remaining Jewish house of prayer in a country which has been a home to Jews for at least two thousand years, the building was of considerable historical significance.
The ownership of the building was also disputed. The Jewish community reported that it had documentation of its original (pre-Soviet) ownership of the building and the purchase of the land on which the synagogue had been constructed. The Head of Religious Affairs at Dushanbe's Department of City Administration countered with two arguments 1) "it is a lie to say that the Dushanbe Jews paid for the construction of the synagogue," and 2) the state owns the land and the building since it underwent nationalisation in 1952 by Soviet authorities.
The government ordered the demolition of the entire Jewish community compound, including the synagogue, in accordance with city center regeneration plans, specifically the construction of the Palace of Nations surrounded by extensive landscaped grounds. The Chief Rabbi of Central Asia, Rabbi Abraham Dovid Gurevich, raised the issue of antisemitism, hinting that there was a feeling that "many people in Dushanbe simply find it unpleasant that a synagogue should stand alongside the palace of nations". In 2004, the US State Department, framed the issue as 'bureaucratic, rather than ideological.' The BBC has reported that, "those opposed to the demolition had been threatened by officials and most of the congregation are afraid to speak out.
The state refused to compensate the synagogue community for the loss of the building, but instead offered 1,500 square metres of land at the edge of the city and rental of a building in which to hold religious services temporarily. The community argued that it could not afford the costs of rental or construction. Even if they could afford these expenses, one source stated that "most of those attending the synagogue are elderly and very poor, and it is hard for them, both physically and morally, to get to a temporary building provided by the city authorities."
UNESCO wrote a letter to the government of Tajikistan in 2004 that destruction of the synagogue would be in "contradiction with international standards for the protection of cultural heritage," but by report did not follow up when they did not receive a reply. UNESCO spokesman Gadi Mgomezulu was quoted as saying in early March 2006 that they "would be following up very closely" on the destruction of the synagogue
In March 2006 it appeared for a short time that the Government of Tajikistan had reversed their decision and would allow the Jewish community to keep the synagogue on the current site. In May 2006, however, it was announced that the synagogue would be rebuilt on "a suitable new site at the center of the city". Still, the Dushanbe Jewish community, spurred by international public opinion, continued its attempts to save the old synagogue on the original site, but in June 2008, the Dushanbe municipal courts finally ruled that the demolition of the old synagogue would proceed as ordered. The court also ruled that the Jewish community would not receive any financial compensation or assistance with the construction of a new synagogue.
The government has meanwhile allocated a plot of 1,500 square meters for the construction of a new synagogue on the banks of the Dushanbinka River in the Ferdowsi municipal district in the west of the city. At the end of June 2008, immediately after the destruction of the old synagogue, Lev Leviev, the President of the Federation of Jewish Communities of the CIS (FJC), confirmed during a visit to Dushanbe that the construction of a synagogue on the new site would begin soon, financed by FJC, the Bukharian Jewish Congress, and private donors.
Tajikistan claims to be a secular state with a Constitution providing for freedom of religion. The Government has declared two Islamic holidays, Id Al‑Fitr and Idi Qurbon, as state holidays. 85–90% of the population of Tajikistan is Muslim, mostly Sunni, roughly 4% are Christian, mostly Russian Orthodox, and less than 1% are Jews. Other small religious minorities include Bahá'ís, Zoroastrians, and Hare Krishna. Muslim and Christian missionary groups have some activity in Tajikistan. The great majority of Muslims fast during Ramadan, although only about one third in the countryside and 10% in the cities observe daily prayer and dietary restrictions.
Relationships between religious groups are generally amicable, although there is some concern among mainstream Muslim leaders that minority religious groups undermine national unity. In 1991, two Bahá'í residents of Dushanbe were shot and killed in 2001 in what was determined to be a religiously-motivated crime.
There is a concern for religious institutions becoming active in the political sphere. The Islamic Renaissance Party (IRP), a major combatant in the 1992–1997 Civil War and then-proponent of the creation of an Islamic state in Tajikistan, constitutes no more than 30% of the government by statute. Membership in Hizb ut-Tahrir (Party of Emancipation), a party which today aims for a nonviolent overthrow of secular governments and the unification of Tajiks under one Islamic state, is illegal and members are subject to arrest and imprisonment. Numbers of large mosques appropriate for Friday prayers are limited and some feel this is discriminatory.
By law, religious communities must register by the State Committee on Religious Affairs (SCRA) and with local authorities. Registration with the SCRA requires a charter, a list 10 or more members, and evidence of local government approval prayer site location. As noted above, religious groups who do not have a physical structure are not allowed to gather publicly for prayer. Failure to register can result in large fines and closure of place of worship. There are reports that registration on the local level is sometimes difficult to obtain.