On 27 June 1997, President Rakhmonov and the leader of the United Tajik Opposition Nuri signed the General Agreement on Peace and National Agreement in Moscow, after the formal end of the civil war in Tajikistan. The Agreement, supplemented by a protocol on military problems signed on 8 March 1997, provided for the legalisation of all parties forming the United Tajik Opposition, the return of refugees and opposition forces stationed in Afghanistan and their integration into the existing army, and the granting of a 30% quota for the United Tajik Opposition in the government and regional authorities. The parties agreed that the National Reconciliation Commission should comprise 26 persons, drawn in equal numbers from the Government and the United Tajik Opposition. Implementation of the agreement did not proceed smoothly and in mid-January the United Tajik Opposition temporarily withdrew from the Commission, accusing the government of deliberately delaying implementation. In order to avoid a further escalation of the conflict, President Rakhmonov had to appoint five representatives of the United Tajik Opposition to the Cabinet on 12 February 1998. By the end of 1998, President Rakhmonov had appointed 14 representatives of the United Tajik Opposition to the Cabinet, although only a few of them held key positions. These included the representative of the Democratic Party, Abdunabi Sattorzoda (Deputy Minister of Foreign Affairs) and Mirzo Ziyoev, a prominent figure in the IRP and leader of the United Tajik Opposition, who wanted the post of Minister of Defence but had to agree to head the Emergency Ministry. At the same time, Akbar Turajonzoda, one of the prominent opposition leaders, was given the post of First Deputy Prime Minister, which he held until 2005.
Separate military confrontations continued throughout 1998. They involved forces close to the government, groups of the United Tajik Opposition and non affiliated fighters. The most serious was the mutiny in Khujand from 4 to 7 November 1998, led by Colonel Khudojberdiev. Some 300 people were killed and some 650 injured in the clashes. Among those involved in the mutiny were former Prime Minister Abdullayanov, his brother Abduga-ni Abdullayanov, former Mayor of Khujand, and former Vice-President Narzullo Dustow.
In the second half of 1999, progress was made on the 1997 agreements. At a meeting between President Nuri and President Rahmonov on 17 June, it was decided to put constitutional reform on the agenda and to continue the implementation of the 1997 agreements. At the beginning of August, Nuri declared that the opposition had achieved its military objectives and that there was no need for military action, which allowed the Supreme Court to lift the 1993 ban on four opposition parties on 12 August 1999 under the 17 June agreement. Six weeks later, on 26 September 1999, a national referendum was held in which 71.8% of the voters who took part approved amendments to the Constitution of Tajikistan. Amendments were made to 27 articles, including permission to form religious parties, a bicameral parliament and the extension of the President’s term of office to seven years.
On 18 October 1999, the IRP declared that it would boycott the presidential elections scheduled for 6 November 1999, mainly because the Central Election Commission did not allow opposition candidates to participate in the elections. A few hours before the elections, the EPI lifted the boycott after Nuri received assurances from Rakhmonov that future parliamentary elections would be held in 2000. Rakhmonov’s only rival was Davlat Usmon, a representative of the EPI, who called the election a farce. Rakhmonov received 97% of the votes.
While some small opposition parties were banned, elections to the lower house of parliament, the House of Representatives, were held on 27 February and 12 March 2000. Despite allegations of campaign and election irregularities, the People’s Democratic Party of Tajikistan and its supporting parties won more than two thirds of the 63 seats. The PDPT won 34 seats, the Communists 13, independent MPs 14 and Islamists only 2. Saydullo Khairulloyev became chairman of the Chamber.
With the holding of parliamentary elections, the transitional period laid down in the 1997 PNC agreement ended and the PDPT held its last meeting and ceased to exist on 26 March 2000. However, a number of problems remained unsolved, including the lack of harmonisation of inter-regional relations.
In the 2000 elections to the House of Representatives, the EPI and the DPT had separate lists, indicating that the United Tajik Opposition was finally disbanded. Although several new parties have emerged since 1997, they have been refused registration by the Ministry of Justice.
Regular elections to the higher legislative bodies were held in Tajikistan in 2005, cementing the dominance of pro-government forces in the power system. The relative stabilisation of the political system was due not only to the targeted activities of the Rakhmonov regime, but also to a number of external factors, in particular the normalisation of the situation around Tajikistan following the defeat of the Taliban regime in Afghanistan, and the SCO countries’ support for Dushanbe in its fight against radical Islamic groups in the region.
Emomali Rakhmonov won the presidential elections again in October 2020.