Very little info is available in English on intra-ministrial decision-making.
Frank Shwartz's dissertation is one, but it merely provides a brief theoretical overview. Namiki Nobuyoshi's book, Tsusansho no Hatan [The Fall of MITI], is the most updated and intersting book, one which discuss the factional struggle within MITI with a lot of empirical details. It is in Japanese. For the earlier period, Shiroyama Saburo's novel, Kanryo tachi no Natsu [The Summer of the Bureaucrats], provides an interesting insight of the factional battles behind the Machinery Industry Promotion Law of 1957 (if I remember the year correctly).
Takasugi Ryo's book, Reppu [The Gale(?)], is another novel which deals with the resignation of Naito Masahisa (MITI International Trade Policy Bureau Chief).

Yoichiro Sato
Department of Political Science
University of Hawaii at Manoa