He resigned office from the safety of his home province of Leninabad.
Ayombekov had been a warlord during the 1992 to 1997 Tajik Civil War between the United Tajik Opposition and the government led by President Rahmon Nabiyev.
President Rahmon Nabiyev and Speaker of the Supreme Soviet Safarali Kenjayev orchestrated the dispersal of weapons to pro-government militias while the opposition turned to rebels in Afghanistan for military aid.
Ethnic groups from the Garm and Gorno-Badakhshan regions, which were underrepresented in the ruling elite, rose up against the national government of President Rahmon Nabiyev, in which people from the Leninabad and Kulyab regions dominated.