Hamilton came from the back of the grid to third thanks to a charging drive and good strategy in Australia, although he also benefited from some of the attrition ahead.
The world champion and his team-mate Heikki Kovalainen had been in the midfield throughout practice and qualifying, and Whitmarsh said McLaren therefore had low expectations for Sepang.
"Frankly I think Malaysia will be very tough for this season," he said. "I think we will improve the car but I think it is a high-speed, technical circuit, we are lacking in downforce at the moment and therefore it is going to be tough."
The team will introduce further new parts at Sepang in a bid to catch up with the frontrunners.
"We have an aggressive development strategy, we have to pick up the performance of the car," said Whitmarsh. "We will have new parts at all of the next races and we have to keep pushing until we are quick enough to reliably score points."
He put the Melbourne result mainly down to Hamilton's driving.
"Overall for McLaren it was better than we could have expected," said Whitmarsh. "A third place, given the performance of the car, shows that Lewis had tremendous discipline.
"I think the team had a good strategy, we took some risks by starting on the softer option tyres, we stopped early enough and thereafter Lewis got stuck in there and did some fantastic overtaking.
"He is unaccustomed to having to drive from the back of the grid like that, but overall it was a demonstration of what a great world champion he is. He did a great job for us today."