We consider the problem of construction and sustainability of cooperative agreements among participants of a conflict-controlled system in the presence of random factors. A method of construction of the cooperative agreements (decisions made in cooperation) is proposed. We also examine the dynamic properties of the agreements allowing to keep cooperation over time. The construction of a mathematical model of the conflict system takes into account random factors affecting the dynamics and payoffs of the participants in the conflict. In the paper the principles of supporting cooperative agreements are formulated. The implementation of such principles allows to guarantee (in some sense) the presence of cooperation over time. The conditions sufficient for the stability of cooperative solutions in stochastic conflict-controlled systems are obtained. The paper also describes some actual problems in this research area.