Just as significant in character, content and scale were the results of the implementation of the Military Protocol. The agreement aimed both to integrate Tajikistan's many armed forces into a unified military and to promote decommissioning and demobilisation. Military cooperation between the parties began before the CNR started operations. They first reached agreement on a ceasefire in the Tehran Agreement of September 1994, which provided for a Joint Commission (JC) of government and UTO representatives to monitor implementation. The experience of working together helped members to progress from barely tolerating their political and military opponents to being able to work together to develop effective solutions to practical problems. Members of the JC, although representing different factions, formed unified teams to negotiate with commanders from the different sides. They often worked in potentially life-threatening circumstances to investigate and prevent violations of the Tehran Agreement. In so doing, many were not only expressing the interests of their own parties but also promoting the interests of the country as a whole. This experience of joint problem-solving between 1994 and 1997created both the mechanisms and habits of working cooperatively and served as a precedent for the work of the CNR.
Implementation of the Military Protocol centred on the deployment of UTO fighters into ten officially established assembly areas where they could be registered for further integration into the Tajik military and other security services. One CNR priority was to draft laws for a general amnesty, which created the legal framework for releasing opposition members from prison and granting amnesty to more than 5,000 UTO fighters. Between July and November 1998, all UTO fighters in Afghanistan were relocated to Tajikistan through the combined efforts of the government, the UTO, the Russian Border Forces and the CIS peacekeepers. At the end of 1998, the UTO leadership announced the closure of all its military training camps abroad.
The next stage was the gradual integration of UTO troops into the national armed forces, partly through the establishment of provisional military units composed of UTO fighters. From early September 1997, one unit of UTO fighters was deployed in Dushanbe. It later became the 25th Battalion. By March 2000 – when CNR activity was completed – 4,498 UTO fighters had been integrated into the armed forces, mostly within their own units. The strategy of retaining separate units was used in the early stages of unification to reduce the potential for tensions between people who had been fighting each other. The greatest levels of integration were achieved in the Committee for the Protection of State Borders because protection of Tajikistan's borders from armed intrusion by foreign forces was a common objective of both the government and the UTO.
While there have been successes in implementing the military protocol, the process was often difficult. It tested the capacity of the political leadership on both sides to control their own military commanders. During the war, the power base of the commanding officers from both sides was not derived from politicians but rather from local people who considered the military leaders as their protectors. The command and control structures were often weak and political leaders had few points of leverage over military commanders. Thus the ending of military confrontation was made possible also by the direct negotiations amongst the commanders themselves. For example, representatives of the government's forces made contact with UTO commanders in the Qarateghin valley in September 1996 and signed the Gharm Protocol. This agreement gave a form of legal recognition to UTO field commanders that signalled the government's acknowledgement of them as partners in the peace process. In turn, these commanders sent a cable to the negotiators at the December 1996 meeting in Moscow and politely but firmly demanded that the negotiators continue their efforts to reaching an agreement. Their action had a positive effect on the UTO delegation's position.
Perhaps the most important condition for the successful implementation of the Military Protocol was the cooperation of the field commanders. The latter were never merely the followers of political leaders; they were a political power in themselves. Most had strong and charismatic personalities and were able to form armed units from people they recruited. They typically enjoyed the full loyalty of those who served with them, as well as the support of the population in the territories they controlled. When these commanders agreed to the peace treaty it was not difficult to convince their fighters to follow, particularly because many were ready for the war to end. Many engaged in direct contacts with their counterparts, which enabled them to gradually develop sufficient trust to address outstanding differences through negotiation rather than armed confrontation. Trust was facilitated by the tendency of military personnel to accord respect to other commanders, in contrast to a shared suspicion of politicians. Cooperation was furthered by the recognition that they could gain more political, social and economic benefits in peacetime than in war. The improving relationship between former military opponents gave further impetus for politicians to continue implementing the General Agreement in order to preserve their political control over the peace process.
Although most UTO commanders supported the peace process, not all were fully content with the practical outcomes. Causes of dissatisfaction included delays in implementing decisions on government appointments, restoring pre-war jobs, closing criminal cases against commanders and fighters to fulfil the amnesty and unreliable distribution of supplies to fighters in assembly areas. In some cases, dissatisfied commanders balked at the integration arrangements and tried to preserve their autonomy. Most such problems were settled by the efforts of senior working groups of CNR members and representatives of the national Security Council and the armed forces. In a few cases, negotiation strategies were combined with the use or threat of armed force to subdue recalcitrant commanders. For example, a decisive test for the newly integrated armed forces occurred in November 1998, when former government and UTO fighters combined to defeat an uprising by the formerly pro-government Colonel Mahmud Khudoiberdyev and his militia in the Leninabad region.