Phadungsil completed 36 holes at 7-under-par 137, which is good for a two-shot lead over Marcus Higley (67), Simon Dyson (68) and Mikko Ilonen (70) at Saujana Golf and Country Club.
Lightning storms hit the course hard while the afternoon wave of players were on the course. Play was called for the day with all 78 golfers returning to the course at 7:00 p.m. ET Friday to finish the round.
This tournament has had its share of weather problems the last two years. In the 2006 event, consistent lightning throughout the week forced the tournament to be shortened to 54 holes.
A pair of Argentineans, Rafael Echenique and Ricardo Gonzalez, are 5 under par for the championship, but did not complete their second rounds. Echenique is 1 under par through 16 holes of his second round, while Gonzalez is 2 under on his round and is on his 14th hole.
Phadungsil began on the back nine Friday and wasted little time in breaking into red figures. He parred 10, but tallied back-to-back birdies at the 11th and 12th holes.
Phadungsil dropped a shot at the par-5 13th, a hole he eagled during Thursday's opening round, but got the shot back with a birdie at the par-4 15th.
The former world junior amateur champion parred five holes around the turn. Phadungsil caught fire again with three birdies in a row from the third, including a 20-footer at the fourth.
He bogeyed the sixth hole, but birdied the seventh for the second consecutive round. That birdie gave Phadungsil a two-shot lead and left the youngster optimistic.
'I hit it so good today,' acknowledged Phadungsil. 'All my shots worked out quite nicely except for my putting which was average. However, most of my birdies were from close range and the only long putt that I had was on the fourth hole.'
Phadungsil, already a two-time winner on the Asian Tour, has enjoyed an amazing career in a short time frame. He burst on the scene with a win at the Double A International Open while still an amateur in 2005, then added another win at the Crowne Plaza Open in China last August.
'I have good memories of playing in Malaysia as it was here that I made my first cut as a professional in last year's event and I finished tied sixth,' said Phadungsil. 'However, I don't really enjoy this course as it's tough. Even if you hit the fairways, you're likely to have an undulating lie.'
Denmark's Soren Kjeldsen shot his second consecutive, 2-under 70 and is alone in seventh place at minus-4.
Kane Webber managed a 1-over 73 on Friday and is in the clubhouse at 3-under-par 141. David Bransdon, Jean-Francois Lucquin and Edward Loar are at minus-3 and have yet to complete their second rounds.
Overnight leader Robert Rock played poorly on Friday. He mixed two birdies, six bogeys and a double-bogey en route to a 6-over 78 and a share of 31st place at even-par 144.