[4] The centre has been embroiled in several controversies regarding the memory of the Holocaust in Lithuania - it is accused by several scholars and Jewish groups of whitewashing the reputation of Nazi collaborators.

[13] In 2002, commemorating the 30th anniversary of Romas Kalanta's self-immolation, Seimas listed May 14 as the Civil Resistance Day (Lithuanian: Pilietinio pasipriešinimo diena) based on recommendations by the centre.

[18][19] In 2007, the head of the Genocide Center at the time, Arvydas Anušauskas, helped launch an investigation into those believed to have participated in the Kaniūkai massacre, including the former director of Yad Vashem and Soviet partisan Yitzhak Arad.

Historian Efraim Zuroff praised the action, but added that “There are other cases that are far more prominent in which the Genocide Center has not chosen to recommend the cancellation of honors.

[25] In 2024 the law on restructuring the Genocide and Resistance Research Centre was passed by the Seimas in July and was signed by the President Gitanas Nausėda.

[26] The Council consists of 11 members appointed for a term of five years: The Council, on the proposal of the Director of the LGGRTC, approves the areas of research, proposes the long-term strategic plan of operations and the annual performance plan, sets annual objectives for the Director, makes recommendations on the management of the Centre, the implementation of the areas of scientific and applied research, and sets the general requirements for the candidates for the Heads of Centre's departments.

[28] During the legal proceedings against Yitzhak Arad, he was heading The International Commission for the Evaluation of the Crimes of the Nazi and Soviet Occupation Regimes in Lithuania.

[5][30] Noreika's granddaughter has advocated for the plaque honoring him to be removed, calling him a "Nazi collaborator who helped murder thousands of Jews and steal their property.

[33] Lukša was accused by eyewitnesses of participating in the Kaunas pogrom - specifically assisting in the massacre of Jews in Lietukis Garage[34][35] and beheading a local rabbi, Zalmen Osovsky.