The Port of Nagasaki was the only seaport in Japan to have trade relationships with countries in Western Europe during the "Period of National Isolation" from the early 1640s until 1858. Today, international cruise ships regularly call at the Port of Nagasaki bringing people who want to visit the city's popular attractions.

In 2008, 32 cruise vessels called at the Port of Nagasaki, including 27 foreign ships and 5 domestic ships.

The Port of Nagasaki's Matsugae International Passenger Ship Wharf is 10 short minutes by taxi from the JR Nagasaki Station (rail) and only three minutes' walk from the Oura Kaigan Dori Tram Station.

The passenger terminal covers a total area of 550 square meters. The passenger terminal in the Port of Nagasaki wharf is 360 meters long with alongside depth of 12 meters, and it has a 20-meter wide apron. The facility includes a 230 square meter lobby, a customs area of 170 square meters, an immigration area of 70 square meters, and a quarantine area of 30 square meters.

The Port of Nagasaki's Ferry Terminal is located in the Mofune area at the center of the port.

The Port of Nagasaki Shipyard & Machinery Works is located in four sites in the city. The main plant opened in 1857 when the Tokugawa Shogunate established the Nagasaki Yotesusho Foundry. The plant contains a 300 thousand ton dry docks that have been used for building, repairing, and converting a range of ships. Northeast of the main plant, the Port of Nagasaki's Saiwaimachi Plant at the Urakami River contains MET turbochargers, foundry shops, and special machinery.

Opened in 1972, the Koyagi Plant is the newest and largest shipyard facility in the Port of Nagasaki. The building has a one-thousand meter long dock where liquefied national gas carriers, liquefied petroleum carriers, and large tankers are built. The Koyagi Plant is the largest in the country, and the facility also manufactures high-performance boilers.

About 25 kilometers east of the Nagasaki Rail Station, the Isahaya Plant in the Port of Nagasaki's Isahaya Industrial Park includes a defense equipment assembly shop, a solar cell factory, and a space equipment shop.

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