Juška was arrested and imprisoned in Kaunas Prison by the Tsarist police as he was suspected as the author or at least distributor of Lietuvos katekizmas. He was further suspected of supporting the rebels, maintaining contacts with them, and encouraging villagers to join the uprising. Residents of Vilkija sent a letter with 72 signatures to , Governor of Kovno, asking for Juška's release. The Russian Academy of Sciences also sent a letter asking for his release as he was working on a much needed Lithuanian–Russian dictionary (in fact, he was working on a Lithuanian–Polish dictionary). The letter achieved its goal and Mikhail Muravyov-Vilensky, Governor General of Vilna, approved Juška's release on 22 February 1864. Juška, in poor health, was released after about nine months in prison. He needed to be put under the supervision of a trusted person, i.e. a parson. Therefore, upon release, he was reassigned as a vicar to Veliuona, but Tsarist police continued to be interested in his activities.
