The article considers the problem of integration of three-dimensional models of potentially dangerous objects in geographic information systems executive agencies of the Bashkortostan Republic. One of solutions this problem is proposed modified integration scheme of three-dimensional models of potentially dangerous objects in Geographic information systems executive agencies of the Bashkortostan Republic, in respect that the integration on data and services levels. To identify closer links between integration objects is introduced a set-theoretic description of the spatial information within the three-dimensional model of a potentially dangerous object and region geographic information systems as a whole. On basis of scheme and description is developed algorithm and interface to work with three-dimensional models of potentially dangerous objects in the Geographic Information System of the executive agencies of the Bashkortostan Republic.