Let KAYAK do the searching
Based on KAYAK hotel searches, the most popular destination is Sasebo (48% of total searches to Nagasaki Prefecture). The next most popular destinations are Nagasaki (45%) 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 $22 (Nagasaki) in the last 3 days. The average price is $140.