The developments of the military intelligence after WWII corresponded directly with the political developments in Czechoslovakia, chiefly with the ever growing influence of the Soviet Union and the takeover of state of the Czechoslovak Communist Party´s in 1948. With respect to the needs of the security apparatus, an administrative separation of the military intelligence took place. The intelligence was still subordinate to the General Staff, but the counter-intelligence was newly incorporated into the structure of the Interior Ministry. These bodies, variously titled, were in operation under this mode until 1990.
In the 1950s, military intelligence went through extensive personnel purges in which the most experienced officers, including František Moravec, had to leave their posts for ideological reasons, often fleeing abroad. The then head of military counter-intelligence Capt. Bedřich Reicin is considered a symbol of these purges. However, the terror he helped unleash was eventually turned against him. Reicin was arrested and consequently sentenced to death in a show trial. After his execution, political trials with purges within the military intelligence were discontinued.
There was long term tension between the army intelligence and counter-intelligence, showing namely in 1968 during the so-called Prague Spring, when the military counter-intelligence approached the new pro-reform course with considerable mistrust, while among the military intelligence and its special units, men like Dubček and Smrkovský enjoyed distinct support. After Warsaw Pact troops invaded Czechoslovakia, the military intelligence command headed by Maj. Gen. Burda assumed a patriotic position, which led to Burda´s removal. However, members of the intelligence did not surrender and continued carrying out activities aimed against the occupants, e.g. by helping provide broadcasting of Czechoslovak Radio, facilitating transfers of journalists in Prague occupied with tanks, and monitoring the movement of Soviet troops.
Also special forces, subordinate to the military intelligence, participated in such operations, such as the 7th Airborne Regiment in Holešov. Its paratroopers not only rejected to collaborate with the Soviet occupants, but also were ready to free Dubček and other Czechoslovak political officials held in Moscow. The regiment suffered the consequences and was, on the pretext of a shake-up, disbanded. Nevertheless, its basis survived this shake-up, as well as the whole normalization era, to eventually lay foundations to today´s 601st Special Forces Group which, until 2014, lay within the Military Intelligence.
New staff purges across the military intelligence bodies marked the beginning of normalization, and cooperation between the military intelligence and Soviet intelligence services further on intensified. Nonetheless, even in these hard times, the Military Intelligence comprised, above all, of experts reaching significant achievements, sparing no efforts to catch up with their western rivals´ technological lead.