In 1851, Niel became a member of the Committee of Fortifications. He became a member of the council of state in 1852 and in 1853 was promoted to general of the division. In the first part of the Crimean War, Niel was employed in the expedition to the Baltic Sea and directed engineering operations against Bomarsund. Early in 1855 Niel was sent to the Crimea, where he succeeded General Bizot as chief of engineers. For some years Niel had been the most trusted military adviser of Napoleon III, and he was now empowered to advise the generals on the spot in accordance with the wishes of the sovereign and the home government.