From rosters I've seen both the JAAF and JNAF the basic formation through the early years was a 3-plane section, the section leader (sho-taicho) and two wingmen. 3 section generally made up a squadron (chutai-buntai), the leader heading the 1st section (Chutaicho-Buntaicho), so on and so forth. (See 'Bloody Shambles' or either 'First Team' volume for Navy. Also if you go to August 05 on this board
http://www.plays.jp/bbs/zero22/index.html you'll find some graphic renditions of early 64th Sentai flight rosters.)
Later, I know for sure that the Navy adopted the 4-plane section having seen several pilot rosters for the Marianas and at Ponape (Avions #149 or 150 lists flight rosters for 5-6 Navy missions covering 38-45 timeframe.) Never seen an Army flight roster from the latter half of the war, so can't coment about that definitively.