On June 14, 1941, during the June deportation, the Soviets arrested him, his wife Emilija, and daughter Raminta. They were separated before being deported to Siberia. Emilija died within 2 years of gangrene from frostbite; Raminta died less than year later of encephalitis. Šilingas learned of their location only after Emilija's death, and he never saw any of his family again. He spent over 20 years in exile: in camps and prisons of Siberia, the last 7 years of his life incarcerated at an Invalid Home in the Ukrainian SSR. At one time he shared a cell with former Lithuanian President Aleksandras Stulginskis and other Lithuanian dignitaries such as Juozas Urbšys, former Foreign Affairs Minister.