At the end of June 1941, a German command headquarters was established in Vilkija, headed by SS Obersturmführer Missenbaum. A detachment of white armbanders was immediately formed. It was led by court bailiff Stasis Gudavičius. On July 7-8, 1941, following Missenbaum's order, the white armbanders’ detachment arrested about 150-200 Jewish men. Most of the arrested were taken to Kaunas, and 21 Jews were shot near Vilkija, close to the village of Jagminiskes.
In August 1941, Vilkija became one of the most important centers for concentrating Jews in the Kaunas region. Jews from other districts were resettled into the Vilkija ghetto. “In the Pakarklė forest in Jaučakiai (2 kilometers from Vilkija), two mass shootings of Jews were carried out. The first was an organized mass murder operation on August 28, 1941, during which 402 Jews were shot, including 76 men, 192 women, and 134 children. The second mass murder occurred at the end of September 1941. On August 28, 1941, Stasis Gudavičius gathered members of his unit (a unit under the command of the German command post in Vilkija) and told them they had to transport the Jews to the Pakarklė forest in the village of Jaučakiai, where pits had been dug. There, an armed unit from Kaunas was to shoot the Jews. Two trucks quickly arrived from Kaunas with about 25-30 – according to other data, about 40 – servicemen from the 3rd unit of the 1st battalion (commanded by Major Kazys Šimkus), led by Lieutenant Juozas Barzda and Lieutenant Bronius Norkus. The warrant officer was Zigmas Arlauskas. When they arrived, 2-3 German officers and several German soldiers were already at the site. Members of the Vilkija command post unit and police guarded the Jews held in the Vilkija synagogue. Together with the battalion fighters, they led about 400 Jewish men, women, and children out of the synagogue and marched them to the site of the mass murder. Some servicemen from the Vilkija unit surrounded and guarded the site, while others brought the Jews in groups to the edge of the pit and forced them to line up. Norkus gave the order to all soldiers of the 3rd unit to shoot the Jews. Soldiers from the Vilkija unit threw the killed into the pit.
One morning at the end of September 1941, about 20 servicemen from the 3rd unit of the 1st battalion and 3-4 German officers arrived at the Vilkija synagogue, where Jews were held. Before their arrival, members of the Vilkija command post unit under the command of S. Gudavičius had already gathered. The head of Vilkija security service, Mikelionis, was also present. Members of the "Vilkija" unit and servicemen of the 1st battalion began to lead women and children out of the synagogue according to the names listed. They forced them to line up in rows of six. They brought the Jews to the site of the mass murder, where a pit had been prepared. Gudavičius, Mikelionis, and the German officers arrived at the site by car. They ordered the battalion soldiers and some members of the "Vilkija" unit to approach the edge of the pit, while the remaining forces guarded the Jews. The Jews were ordered to undress and hand over all valuables. Then they were led in groups to the shooting site. Gudavičius, Mikelionis, and the German officers gave the order to open fire on the battalion servicemen and members of the "Vilkija" unit. They killed the Jews from 8:30 a.m. until 1:00 p.m.
On December 4, 1945, according to information contained in the documents of the chairman of the Vilkija Executive Committee Skaudis and his deputies Armanis and Beržanskas, up to 800 murder victims were found in a mass grave in the Pakarklė forest in the village of Jaučakiai. In 1958, the remains of Soviet activists, communists, Jews, and others from the Veliuonai, Seredžius, and Čekiškė districts, killed between 1941 and 1945, were transferred to the mass grave in the Pakarklė forest in Jaučakiai. The remains of about 3,500 people were buried in the common grave.
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