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"You're playing a Links out there and it's playing like a parkland, so it's quite disappointing the way they are setting it up," Goosen said on Friday.
"I mean, that's why there's so much low scoring out there.
"No wind, the course is drenched and guys are shooting eight, nine under."
The two-time US Open champion was not in awe of Nicolas Colsaerts' course record nine-under-par 64 in the first round, and said it was down to the soft greens.
Traditionally, Links style golf courses play hard and fast, and Goosen said Fancourt was not playing to expectations.
"It's extremely soft. I'm quite surprised. It's not the Links as we know it," he said.
"I had two tee shots today that came back on the fairway, and yesterday [Thursday] I had another that had mud on it.
'The Goose', who has not won on the European Tour since his victory in the Qatar Masters back in 2007, improved from a first-round 71 to trail leader in fellow South African, Branden Grace, by six shots going into the weekend.
"I had more consistency and I got off to a nice start," said Goosen.
Goosen, however, threw in two bogies in his last five holes and failed to birdie the par-five 18th.
"It was the same as yesterday(Thursday) - a disappointing finish," he said.
"It could have been a lot lower round."
Goosen, 42, won the SA Open on the Links in 2006, beating Ernie Els down the stretch, but would have been hoping for a radical turnaround for another victory on the course.
The forecast for the weekend predicted little wind, which would take away the advantage of the local players with experience at Fancourt.
"It doesn't look like it's going to blow at the moment," Goosen said.
"You can probably expect a low winning score around here."
