Her lawyers said they submitted the appeal to human rights ombudsman Vladimir Lukin, who said he'd give his full support to the application, the Russian daily Vedomosti reported.
The appeal to the Supreme Court comes as the precise whereabouts of Tolokonnikova, 24, are unknown, RIA Novosti said. She was transferred from a women's prison camp in the Mordovia region to a prison colony in Siberia, her husband, Petya Verzilov, said.
Tolokonnikova was moved after going on a hunger strike over conditions in the Mordovia prison, RIA Novosti said. In an open letter, she described a forced-labor routine that included 17-hour work days and a variety of punishments.
Tolokonnikova said after she wrote about the conditions, prison officials put her in an "information blockade." On Oct. 21, the prison service said she was being transferred out of the women's prison camp but didn't say where.
Neither Verzilov nor Tolokonnikova's lawyers have had contact with her since, RIA Novosti said.
Tolokonnikova and Pussy Riot bandmate Maria Alyokhina are serving two-year sentences for hooliganism motivated by religious hatred for a performance in Moscow's main cathedral in February 2012. A third band member, Yekaterina Samutsevich, was tried and released on appeal.