A couple of people compare this earliest adaptation of Shusaku Endo's 1966 novel with Scorsese's, which is rather strange because Shinoda Masahiro is one of the most important directors of the Japanese New Wave, on a par with Nagisa Oshima and Shôhei Imamura - almost as influential for Japanese cinema as Scorsese himself has been. Oshima is popular in the West because his films emulate the Nouvelle Vague, and Imamura won the Golden Palm twice because of his universal approach to class struggle. Shinoda is more difficult to relate to because he relies on cultural metaphors which are difficult to decipher for foreigners.
"Silence" is not his best film if you know the novel, for which Endo was long expected to receive the Nobel Prize. The book describes the story of two missionaries arriving in Japan after the ban on Christianity matter-of-fact from the perspective of the priest Rodrigo, who undergoes a transformation from spiritual idealization to materialistic resignation. Shinoda faithfully adapts the dialogue-heavy plot and adds color symbols and a good deal of sadistic voyeurism, but this doesn't work well. There is too much contrast between intellectual discourse and violent imagery, although the idea might be that you cannot reconcile the two.
What makes "Silence" still more interesting than Scorsese's film is the perspective. Instead of foreigners observing their Japanese surroundings, it is the Japanese class system which observes the foreigner, and his ultimate capitulation derives from realizing that he can not be a subject, only an object of his faith.