Headed by Army Gen. Andrey Ivanovich Nikolayev, the Federal Border Service is an independent agency that is directly subordinate to the Russian President. It includes an Intelligence Directorate and a secret service unit. Although administratively separate, its headquarters is located in the former KGB Lubyanka headquarters also occupied by the SVR.
The Military Council of the Russian Border Guard troops is responsible for measures for strengthening of the Russian state border, including relations with other CIS members to enhance the protection of the Southern borders of the Commonwealth.
The FPS is organized into six border districts, three groups of border troops within the territory of Russia, the groups of RF border troops in Tajikistan, Kyrgyzia, Georgia, Armenia, and the independent operational group of Russian border troops in Turkmenia. These forces include 63 border detachments, four independent border komendaturas, 17 naval formations and units, the Amur Border River Flotilla, 10 aviation regiments, an independent border monitoring detachment, 30 independent entry control points, and also communications, rear services, and technical support units and institutions.
As of August 1996 Lt. Gen. Vladimir Rozhkov was chief of the Russian Federation Federal Border Service Intelligence Directorate and deputy commander in chief of the Border Troops. He replaced Lieutenant General Aleksandr Aleksandrovich Bespalov, a graduate of the USSR KGB Higher School, who was chief of the Intelligence Directorate as of 1994.
Each border district has an intelligence section, whose chief is deputy commander of the district. The border detachments have intelligence sections. Staffers were formerly trained at the Foreign Intelligence Institute and the KGB Higher School. An intelligence faculty has been set up under the Border Troops Academy.The Intelligence Directorate of the Russian border troops is explicitly authorized through law with responsibility over foreign country intelligence, to protect Russian state borders, the economic zone as well as the Russian territorial waters from intelligence acquisition by foreign countries. The FBS intelligence activities extend to everything relating to the border regions of Russia. In May 1996 FBS leaders asserted that the expansion the NATO create a new threat along the Russian western boundary that would require the FBS to implement appropriate counter-measures. The Intelligence Directorate has been active in coordinating efforts with the border guard departments of Kazakhstan, Kirgizia, Russia, Tajikistan, and Uzbekistan in working to close the Tajik-Afghan border to penetration by insurgents and drug traffickers from Afghanistan.