Yui Ueda followed his opening 8-under 63 with a 67 to remain atop the leaderboard and teenage phenom Ryo Ishikawa missed the cut by two shots at the Tsuruya Open on Friday.
Ueda had six birdies and two bogeys to reach 12-under 130, three strokes ahead of New Zealand's David Smail, at Yamanohara Golf Club.
Smail made a double eagle on the par-5 15th hole and matched the day's low round with a 64.
Shingo Katayama and Masaya Tomida both shot 66s to tie for third at 8-under.