In 1885, the Japanese government persuaded the French Génie Maritime to send Bertin as a special foreign advisor to the Imperial Japanese Navy for a period of four years from 1886 to 1890. Bertin was tasked with training Japanese engineers and naval architects, designing and constructing modern warships, and naval facilities. For Bertin, then aged 45, it was an extraordinary opportunity to design an entire navy. For the French government, it represented a major coup in their fight against Great Britain and Germany for influence over the newly-industrializing Empire of Japan.

While in Japan, Bertin designed and constructed seven major warships and 22 torpedo boats, which formed the nucleus of the budding Imperial Japanese Navy. These included the three Matsushima-class protected cruisers, which featured a single but immensely powerful 12.6-inch (320 mm) Canet main gun, which formed the core of the Japanese fleet during the First Sino-Japanese War of 1894–1895.