The Australian carded a five-over-par 77 on Saturday to fall to four over for the tournament and out of contention.
He was penalised a shot at the 13th hole when officials deemed the ball moved after he addressed it with the club on the fairway.
Lee copped the penalty on the chin but was clearly miffed by suggestions of slow play, explaining that the extended 20-minute gap imposed to the group ahead of them had exaggerated the issue.
"They (Masters scheduling officials) gave us (Lee and playing partner Harris English) the gap between two of the groups," he told AAP.
"It just looked bad on us, and the guys right behind were playing fast and so it looked terrible."
Lee began well, scrambling a par from the trees and sand on the first and then moving to two under with a birdie on the third.
He almost holed out for eagle on approach to the fifth, but then three-putted to take bogey in a sign of things to come.
"It was okay for the first bit and we were on the clock and I think that got to me," he said of his putting.
"We had a 20-minute starter gap, which doesn't look good for us and the ref said we were a minute behind as soon as we saw him.Â
"And the next hole we got timed.
"Playing Augusta is already tough ... we played nine holes in two hours which is apparently really slow.
"That was tough and it just got to me."
Lee, a winner on the PGA Tour last month, is keen to wipe the slate clean for Sunday's final round.
"I'll definitely learn from it and just good golf (tomorrow); we'll stick to our process and see what happens," he said.
16°C