Notaras served briefly (6–16 April 1826) as President of the Third National Assembly, but its sessions were suspended at the news of the fall of Missolonghi. He remained head of a provisional committee representing the Assembly to the Executive, and on 16 March 1827 issued the order reconvening the Assembly at Troezen. Due to his involvement in a scandal in support for his nephew Ioannis Notaras, he was dismissed from his post before the Assembly reconvened, and retired from public life for two years. Under the new Governor of Greece, Ioannis Kapodistrias, Notaras became a member of the Panellinion, an advisory body created instead of a parliament, but was not very active there. On 27 November 1829, Kapodistrias appointed Notaras as president of the Court of Appeals in Nafplion.