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Based on KAYAK hotel searches, the most popular destination is Nagasaki (50% of total searches to Nagasaki Prefecture). The next most popular destinations are Sasebo (42%) and Shimabara (4%). Searches for hotels in Unzen (3%) are also popular.
KAYAK users have found double rooms in Nagasaki Prefecture for as cheap as $28 (Tsushima) in the last 3 days. The average price is $111.