The Reserve's Area Protection Department carries out the main activities of the Reserve such as preservation of the area in its natural state and control over compliance with the established regime. To perform these tasks, the Reserve has a protection service consisting of state inspectors for environmental protection. In 2016, the staff of the Department of Protection was made up of 20 persons, and the structure of the Department includes 3 subdivisions, which are forestry "State Natural Biosphere Reserve Kerzhensky" (9 staff members), task force (6 staff members), and fire-chemical station (FCS-I) of the I type (5 staff members).
The Department of Protection was established and started working soon after the Reserve was established, in the summer of 1993. The main task of the Reserve's protection staff was to establish the boundaries of the reserve and to inform the visitors of the Reserve about the boundaries and the established regime. After the billboards and barriers were installed and the explanatory work was carried out, the inspectors began to prevent violations, draw up administrative protocols, and seize tools and products of illegal use of natural resources.
The establishment of the protection regime of the Reserve lasted for the first 2-3 years. During this time, the issue of resettlement of the families of the majority of citizens living in the Reserve was resolved, land management works were carried out, and zoning of the Reserve's territory was established. The Reserve's staff has gone through numerous lawsuits and "terrorist acts" against the Reserve's property. The number of detected violations of the regime has decreased from 150 to 200 per year to 40 to 50 per year.
In 1998-2000 the forest inventory was carried out in the Reserve, which made it possible to plan and implement the necessary forest management measures. On February 29, 2008 the order of the Federal Forestry Agency No. 59 "On Determination of the Number of Forestry Enterprises in the State Natural Reserves and National Parks and Establishment of their Boundaries" established the State Natural Biosphere Reserve Kerzhensky Forestry Enterprise.
The territory of the forestry division is divided into twelve rounds, united into four inspection areas. The forestry infrastructure includes about 150 km of patrol roads and 6 cordons. The forest area is divided into 210 blocks of approximately 1 by 2 km in size.
In addition to the territory of the Reserve, the security department monitors the state of the protected area of the Reserve with the area of 10660 hectares, located in the territory adjacent to the Reserve Voskresensky district forestry.
Besides carrying out the main tasks, the staff of the Department of Protection constantly participate in the work of other departments of the Reserve. The inspectors carry out a significant amount of monitoring activities, in particular, phenological observations, registration of mammals, chickens, collection of information on meetings of animals and plants in the Reserve. The Reserve's inspectors protect scientific hospitals located in its territory, as well as assist colleagues from the Scientific Department in carrying out research. The inspectors, together with the environmental education staff, regularly work with volunteers, visitors to the Reserve, and sometimes with tourists. Environmental education of the protected area violators is almost entirely the task of the Department of Protection.