Based on the document, the National Reconciliation Commission was established. Representatives of the opposition, mainly, Islamic Renaissance Party, received 30 per cent of public offices. The amnesty was carried out for oppositionists, and opposition parties that used to be prohibited were legalised. Tens thousands of Tajik refugees returned to the country.
However, the agreement on peace could stabilise the situation only to some extent. By then, the relations between President Emomali Rakhmon and his allies from the People's Front became strained.
Back in January 1996, Makhmud Khudoberdyev, the influential commander of the People's Front, delivered the ultimatum to the central power and threatened to invade Dushanbe. Authorities eventually managed to force him out to Uzbekistan, but in November 1998, Makhmud Khudoberdyev committed a large-scale invasion to the north of Tajikistan. Fighters of the former opposition took place in the subjection of the rebellion.
In August 1997, after armed clashes in Dushanbe, another influential figure of the People's Front, ex-minister of interior affairs Yakub Salimov was
neutralised. He left the country, but he was arrested and
convicted afterwards. Applying the carrot and the stick approach, the central power managed to disarm or even destroy the armed opposition – both new and old – by early 2000s. Thus, the 'man with a gun' factor was
minimised.
In November 1999, President Emomali Rakhmon
won the presidential election with 97.6 per cent of votes, almost with no challengers. Davlat Usmon, an opposition candidate of IRPT, could not even
gather 145,000 signatures necessary for registration.
Previously, the country held a referendum on amendments to the Constitution, which increased the presidential term of office from five to seven years (the president could be elected for one term only). Also, a two-chamber parliament was established and headed by ex-mayor of Dushanbe Makhmadsaid Ubaidulloev, and registration of religious political parties was allowed.
By results of the 2000 election, militants could not
make it to the Madzhlisi Namoyandagon, the lower house of parliament. The parliament was already under full control of President Emomali Rakhmon and only two deputies from the recently legalised opposition Islamic Renaissance Party of Tajikistan could make it to the parliament. According to Tajikistan-based journalist Radzhab Mirzo, the 2000 parliamentary election actually meant the defeat of the opposition as no prominent secular oppositionist could become a deputy.
"In fact, the examination of political forces began during the 1999 presidential election. The government then realised that opposition forces could not build the real coalition due to serious contradictions regarding a range of political issues (attitude to secularism and religion) and division of power," said Radzhab Mirzo meaning that members of IRPT received public posts under the 30 per cent quota. The central authority managed to consolidate their position in the regions, although local informal leaders, who competed with central power, maintained their influence locally, especially in Gorno-Badakhshan Autonomous Region.