Flooded fairways and unrelenting rain has forced the Australian PGA Championship committee to abandon play on day two and reduce the $2 million showpiece to a 54-hole event.

There will be no play on Friday at Royal Queensland with officials initially suspending action before making a definitive call at 11.30am (AEST) as further storms pounded the riverside Brisbane course.

Players will return on Saturday to play their second rounds before the field is cut and a third and final round is contested on Sunday.

More than 200mm of rain fell in Brisbane this week with ground staff working overtime to ensure play was possible on Thursday.

The forecast is more encouraging for the weekend.

Finishing the event on Monday remains a consideration, but not an ideal one given the Australian Open begins in Victoria on Thursday.

Elvis Smylie (six-under 65) heads a packed leaderboard, one clear of French star Victor Perez, Australian Matias Sanchez, Swiss talent Joel Girrbach and Chile's Cristobal Del Solar, who birdied four of his last five holes in driving rain on Thursday afternoon.

Local drawcards and major winners Cameron Smith and Jason Day, in his first Australian event in seven years, are two shots behind Queenslander Smylie.

Min Woo Lee (three under) is the defending champion and will be in a Saturday afternoon marquee group with Smith and Day.

"There's probably a sense of relief a bit from the ones that would have been going out," PGA of Australia tournaments director Nick Dastey said.

"It's no secret it was a bit harder out there (on Thursday afternoon) ... and they've been up early, waiting."

Dastey said the greens had held up "unbelievably well", with water-logged fairways on the front nine the major concern.

"The golf course is just not getting a chance to dry out and get to a position where we're even looking at getting any reasonable play where it's fair and equitable," he said.

"Disappointing, but it does mean we have a massive weekend of golf.

"We have the Australian Open to think about ... the players have to get down to Melbourne and prepare for that.

"The course staff have done an incredible job ... throughout the nights for the last four or five days."