Tokyo, Sept 21, 2012 (AFP) - Fujita, a two-time winner on the Asian Tour, carded a three-under-par 68 for a one-shot lead over Pagunsan, who birdied the last three holes for 66. He was tied in second with Darren Beck of Australia and Koumei Oda of Japan.
India's Shiv Kapur battled fatigue and jetlag for 68 and was three shots off the pace, followed by Asian Tour rookie David Lipsky (64) of the United States and Japanese prodigy Ryo Ishikawa (65), who were a further shot back.
Overnight leader Yuta Ikeda, who shot an opening-round 62, slipped back with a 76 for tied 24th place at the Higashi Hirono Golf Club.
With him were Jeev Milkha Singh of India and Thai duo Prayad Marksaeng and Chinnarat Phadungsil at the 150-million-yen (about $1.9 million) event sanctioned by the Asian Tour and Japan Golf Tour.
"My putter went cold on the back nine and I couldn't score," Fujita told the Asian Tour after his birdie on the last hole saw him sitting top of the pile.
"It was quite disappointing but this is just the second day and we do not know how it will turn out in the end," said Fujita, who won in Japan last week.
"The course set-up might get tougher in the last two days so I hope I can continue shooting in the 60s.
"Last week's win has boosted my confidence but like I said, it is still early in the tournament and there are many good players behind me."
The sweet-swinging Pagunsan got off with a bogey, birdie and bogey start but steadied ship with six further birdies including a missed eagle opportunity from 25 feet on the 18th hole.
"My approach shot landed on a slope (18th) and the ball could have rolled into the water but it went towards the green instead. I had a chance for eagle but settled for an easy birdie instead. I'll take that," he said.
Scores after round 2 of the Asia-Pacific Panasonic Open (par 71)
132 - Hiroyuki Fujita (JPN) 64-68
133 - Darren Beck (AUS) 68-65, Juvic Pagunsan (PHI) 67-66, Koumei Oda (JPN) 64-69
134 - Masamichi Uehira (JPN) 66-68, Hideto Tanihara (JPN) 67-67, Yusaku Miyazato (JPN) 64-70
135 - Shiv Kapur (IND) 67-68, Daisuke Kataoka (JPN) 67-68, Masahiro Kawamura (JPN) 70-65, Tomohiro Kondo (JPN) 66-69
136 - Shigeru Nonaka (JPN) 66-70, Wu Ashun (CHN) 67-69, Toru Taniguchi (JPN) 67-69, Lee Seong-Ho (KOR) 67-69, Tjaart Van Der Walt (RSA) 68-68, David Lipsky (USA) 72-64, Ryo Ishikawa (JPN) 71-65