Okabe Nagatsune was appointed the Magistrate of Nagasaki (1857). He signed a Japan-Dutch commerce treaty with a Dutch delegation (1858).
Opened an English language school in the compound of his residence. When a Russian fleet arrived, he set up a rest house for Russian seamen at the request of the Russian fleet commander, in cooperation with Ryojun Matsumoto, physician. This was the first venereal disease examination system adopted in Japan. In 1861 Okabe Nagatsune established a clinic for general patients as well as for the destitute. The clinic was under the direction of Johannes Pompe van Meerdervoort a Dutch physician. It became the mecca for Japanese medical students.
It was during his administration that Nagasaki became an open port. The foreign residential quarters were enlarged, the fumie (the method of finding Christians by forcing people to tread on tablets representing the crucifix) abolished, casting of cannons started and chemical research encouraged by Nagatsune. Although his progressive ideas were assaulted by diehard anti foreign samurai. He was promoted to Magistrate of Foreign Affairs (1861). Was appointed Police Inspector General of the Shogunate (1862).