The USSR's Communist Party and the government called on the KGB to maintain an enhanced counterintelligence posture at nuclear facilities. A 1947 resolution of the USSR Council of Ministers regarding security at the warhead R&D facility in Sarov, for example, directed that, "[I]n order to prevent infiltrations of Object No. 550 (code-name of the R&D center] by spies, saboteurs, and other enemies . . . the USSR Ministry of State Security (comrade Abakumov) is obligated to step up its operational and chekist work at Object No. 550 and in the areas of Mordov republic and Gorky region adjacent to the special regime zone."

In response, the KGB established a Department K in its headquarters in Moscow and "K" units in the regions. The KGB worked with nuclear facilities to develop suitable cover stories to conceal their true missions, monitored information protection measures, and implemented countermeasures against technical collection systems (see below). It also conducted classic counterintelligence operations involving the penetration of foreign intelligence organizations, working against suspected and confirmed foreign intelligence officers in the Soviet Union, and monitoring nuclear facilities and their surroundings.

According to KGB analysis, its success in preventing the insertion of clandestine agents inside the Soviet Union from the late 1940s to early 1950s forced Western intelligence services to rely on intelligence officers operating under diplomatic cover and agents entering the country via such other legitimate channels as tourism, scientific meetings, and cultural exchanges. This allowed the KGB to focus its operational resources on a relatively small number of targets. In 1961, KGB surveillance against Canadian and British diplomats led to the exposure of Col. Pen-kovskiy, who had provided the West with information on a range of nuclear-related matters. Later on, according to the KGB's 1967 Annual Report:

The effectiveness of the KGB's counterintelligence operations, on one hand, and improvements in US signals intelligence, overhead imagery, and nuclear test monitoring capabilities, on the other hand, led the US atomic energy intelligence program to rely increasingly on technical collection systems. KGB historians observe that the 1950s marked the beginning of the massive use of novel espionage technologies. In the nuclear energy area, for example, "[T]o locate Soviet atomic facilities . . . American, British, and Canadian intelligence officers and their agents were armed with state-of-the-art radio-electronic equipment, . . . radio-navigational systems . . . . Massive application of modern means of science and technology was a characteristic feature of activities by imperialist intelligences during that period [1953-58]."

In response, the KGB "took measures . . . to bring to further perfection the protection of state secrets from the radio-technical and aerial-space means of reconnaissance of the enemy." At a test site, for example, operations on nuclear devices in the field were conducted under a tent to prevent visual observation. Furthermore, "[T]he organs of military counterintelligence of the KGB did significant work on camouflaging . . . depots of nuclear weapons and other objects from the enemy's space reconnaissance." Moreover, most communications between nuclear facilities and the complex's headquarters in Moscow were by teletype or telephone and involved the use of landlines and microwave systems. These were considerably more difficult to intercept than short-wave radio transmissions, the target of the National Security Agency's listening stations at that time. Particularly sensitive documents, such as production data for the nuclear warhead assembly complex, were hand-delivered by couriers.

Radiological analysis of radioactive residues from Soviet atmospheric tests, collected by the US atomic Energy Detection System (USAEDS), was the primary tool for tracking the progress of the USSR's nuclear weapons R&D program and its atomic capabilities during the 1950s and 1960s. Indeed, benchmarked by US nuclear test data, the analysis of Soviet nuclear test residues allowed scientists from US national laboratories to determine the Soviet devices' "design space," yield, efficiency, materials, and other parameters. After 1963, when the United States and the Soviet Union signed the partial test ban treaty prohibiting nuclear explosions above the ground, each country made a transition to underground nuclear testing. The end of atmospheric testing was a major setback to the US intelligence effort. According to National Intelligence Estimate 11-2A-65, "[O]ur estimates of Soviet nuclear weapon technology . . . are based almost entirely upon analysis of the tests through 1962 . . . and upon extrapolation from that analysis." The radiological method remained useful to some extent because of radioactive venting from Soviet underground explosions. However, Soviet efforts to reduce venting eventually made the US radiological method ineffective against Soviet targets.

In 1973, the increasing threat from Western technical collection systems caused the Soviet government to establish a new organization, the State Technical Commission, with the main mission of developing and implementing a comprehensive system of countermeasures against technical espionage.

During the Cold War, US intelligence agencies invested considerable resources and effort to understand and predict Soviet nuclear technologies and policies. Despite the fact that the United States was off by several years in predicting the first Soviet atomic explosion in August 1949, it subsequently enjoyed numerous and remarkable achievements. For example, from the first Soviet explosion through the test series of 1961-62, US intelligence detected and correctly characterized many milestone designs of Soviet fission and thermonuclear weapons. Much of this success was based on the fact that atmospheric nuclear explosions by nature were so powerful that they were physically impossible to contain or conceal.

The Soviet Union also was unable to hide from overhead imagery systems its huge nuclear weapons production infrastructure. By 1965, the US intelligence program had correctly identified and characterized facilities with more obvious nuclear signatures, including all fissile material production centers, some uranium processing facilities, the Sarov warhead R&D center, the serial warhead assembly facilities in Lesnoy and Trekhgorny, and the component manufacturing plant in Zarechny. It appears that some facilities, especially those lacking distinct signatures, escaped detection. It is not clear, for example, that the CIA was aware in the 1960s of the non-nuclear warhead component manufacturing facilities and R&D institutes in Moscow, Yekaterinburg, Novosibirsk, and Nizhni Novgorod.

Soviet D&D measures were very effective in preventing the United States from learning what was going on inside the buildings it could easily see from space. For example, US intelligence had a hard time assessing the Soviet program to produce enriched uranium for nuclear weapons and reactors. According to a 1954 National Intelligence Estimate:

More than 10 years later, in 1965, US intelligence observed that while it had reasonably accurate estimates of power inputs into the Soviet gaseous diffusion plants—based on data obtained from overhead imagery and electric grid analysis—its assessments of plant efficiencies and, as a result, production capabilities, were very uncertain. Reliable estimates of plant efficiency would have required detailed knowledge of the Soviet gaseous diffusion technology and plant operations, which stand-off collection systems simply could not deliver.

Perhaps even more importantly, the USSR succeeded in preventing US intelligence from detecting its transition to the more advanced centrifuge uranium enrichment technology. A 1964 National Intelligence Estimate judged that "[T]he present size of the Soviet gaseous diffusion complex . . . tends to indicate that significant U-235 production by the ultracentrifuge and other methods is unlikely." In fact, a pilot centrifuge facility had begun operation in Novouralsk in 1957. By 1962, the initial phase of a much larger complex at that site had commenced operations, and by 1964 the entire industrial centrifuge enrichment facility had been completed and was fully operational.

The Soviet government worked hard to keep the centrifuge effort secret. The critical point was the repatriation of the German scientists who had participated in the project. According to Nickolai Sinev, the Soviet chief centrifuge designer during the 1950s:

Another participant in the centrifuge program adds bitterly that "the damage to morale and economic damage done by the notorious regime of secrecy, which did not allow the USSR to patent abroad the Soviet centrifuge design, was [enormous]."

Throughout the Cold War, the United States and its allies mounted a massive atomic energy intelligence effort against the Soviet Union. It was countered with a highly effective, defense-in-depth system of countermeasures. The precise score of this competition is unlikely ever to be established. It is clear, however, that long-range, stand-off technical systems proved to be the best collection sources for the United States, allowing for successful tracking of many aspects of the Soviet nuclear program. Overhead imagery enabled the detection and analysis of critical elements of the Soviet nuclear infrastructure. The USAEDS system, designed to monitor radioactive effluents from nuclear explosions and nuclear material processing, yielded important data on the development of Soviet nuclear weapons science and technology. Because of denial and deception countermeasures, however, the USSR's nuclear program was an exceptionally hard target. The lack of reliable on-the-ground intelligence made it difficult for the West to understand important developments inside the Soviet nuclear complex, which resulted in significant intelligence gaps.