During July 1944 – January 1945 the Red Army retook the entire Lithuanian territory and proceeded to re-implant the Soviet administration which had fled in 1941. In the second half of 1944 Soviet institutions, including the People’s commissariat of agriculture and the People’s commissariat of state grain and animal farms, resumed their activities. During first years of the second Soviet occupation, state bodies, administering the agricultural sector, underwent numerous reorganization, their nomenclature and structure were in constant flux. In 1946 after the reorganization of people’s commissariats into ministries, state authorities set up three ministries – ministry of crop production, ministry of animal husbandry and ministry of technical crops. On February 27, 1947 the first to ministries were amalgamated into one Ministry of Agriculture, and on March 19, 1947 the new Ministry of Soviet State farms was set up. Anyway, the most important decisions concerning all spheres of life in occupied Lithuania, including agriculture were taken not in these local bodies but by the central leadership of the Communist Party in Moscow.
Soviet occupational administration resumed the divisive “land reform” which they have started in 1940, however the armed resistance of nationalist guerillas which included large masses of farmers in its ranks, forced occupants to postpone collectivization for several years. Once again, the soviet pursued their policies of confiscations of movable and non-movable property of farmers, and imposed heavy burden of monetary and natural taxes. In 1947 the policy of the destruction of economically more viable farms took full speed, paving the way force forcible process of mass collectivization. If means of economical repression yielded no effect, occupants resorted to naked and brutal violence. Once of the most merciless means of intimidation were mass deportations of farmers and their families to Siberia and other regions of the Asiatic part of the USSR. In 1948 alone the number of deportees exceeded 70000 people and 98.3% of them were farmers and their families.
Especially hard the Soviet reprisals hit economically strong farmers who, according to the communist ideology, were called “kulaks” (exploiters of people). The number Lithuanian farmers decreased by 44000 or 9% during 3 postwar years. In 1948 the Communist Partly overtly started the forced collectivization campaign. Until 1952 it was completed, about 400000 private farms were merged into state farms(sovkhozes) or collective farms(kolkhozes, which theoretically were run by the “collective” of peasants but in fact were just another name for state farms and their “members” nothing more than simple agricultural workers). The agricultural production decreased dramatically, hundreds of thousands of hectares of agricultural land were left and grew with bushes and shrubs. Newly established kolkhozes were many times reorganized, the most often new larger farms were created from the amalgamation of smaller ones. The forced collectivization pushed Lithuanian countryside towards greatest economical collapse and social degradation. The economical indicators in 1956-58 were still below of those before 1940.
The Ministry of Agriculture was reestablished again in 1965, after the reorganization of the former Ministry of Agricultural Production and Supplies. In 1985 the administration of the agricultural sector in the USSR was restructured again, and the new administrating body was called the State Agro-industrial committee on the USSR level and State agro-industrial committee of the Lithuanian SSR (officially set up in December 16, 1985) on the “republican” (local) level. This structure lasted until October 1, 1989. During the period of Soviet occupation the ministry was many times renamed and restructured. During much of the Soviet period there were not one but several bodies administrating different subsectors of the agriculture and food sectors. The changes of top administrators were also frequent, although there were exceptions, as agronomist Medardas Grigaliunas who held the charge of minister during 23 years. Both he and his predecessor Vytautas Vazalinskas were considered by their contemporaries outstanding personalities of their time who were able to bring some positive changes in agriculture and rural sector.