Hydrofoil is a high speed boat which uses hydrofoil technology; lifting a surface that operates in the water. Due to Japan is surrounded by sea, hydrofoils are very important means of transportation. Then, please note that there are high speed boats which do not use hydrofoil technology too.
There are 6 maritime transport companies which operate total 7 domestic regular routes. 4 routes are connecting ports in Honshu and offshore islands, the other 3 routes are connecting ports in Kyushu and offshore islands. Unfortunately there are no hydrofoil route from Shikoku or Hokkaido. Probably hydrofoils connecting Kagoshima and Yakushima island is familiar for foreign tourists. Then, there is also one international route between Fukuoka and Busan in South Korea.
All those routes are operated also by ferries, which can carry vehicles. Then, the vessels are larger but slower. Which means the fares are cheaper than hydrofoils.