After the secessionist war broke out in Abkhazia in 1992, Kvitsiani organized a militia force of several hundred fighters named "Monadire" ("the Hunter") in the upper Kodori valley in order to fend off the Abkhaz threat. He succeeded in keeping the strategically crucial gorge under the control of his militia after the retreat of the Georgian forces from Abkhazia in 1993, though militia in the area reportedly also demanded money and possessions from fleeing civilians, in exchange for passage. Following the war, Kvitsiani maintained nominal dependence on the central government of Georgia. The then-President of Georgia Eduard Shevardnadze attempted to channel Kvitsiani's activities into the legal framework of the Georgian state apparatus. Kvitsiani was appointed deputy special state envoy to the Kodori valley in 1997 and then special state envoy to that area in 2000. He and his men entertained good relations with the Abkhaz people despite numerous skirmishes and incidents occurring over the years. According to his own claims, Abkhaz representatives occasionally tried to persuade him to sign a four-sided treaty that would effectively transfer control of the valley over to the Sukhumi administration. Kvitsiani however always refused and also countered various armed incursions, mostly in a pacifying manner. He earned the Abkhazians respect by treating prisoners well and in some cases even releasing them with their arms returned. In 1998, his militia was made a special battalion of the Georgian Armed Forces, but the government had little control of it. In 2004 on behalf of the Georgian government Emzar Kvitsiani was also engaged and partially responsible in convincing the Abkhazians to clear minefields that were deployed during the war. In return minefields laid by the Georgian army would be removed as well.