Whincup was 18th in the day's earlier session and was blunt about his and engineer David Cauchi's lack of progress in today's two hours of running time.
"Today didn't go very well at all," Whincup said.
"We just have no pace, which has continued on from Perth.
"We seemed to be on track during the session, then we put our set of green tyres on and we were almost last, so I don't know.
"It's not really making sense at the moment."
The team will continue to analyse the data overnight, with a brief 15-minute practice session tomorrow morning to confirm any changes before the two back-to-back 10-minute qualifying sessions.
"We'll keep doing what we do and working hard to fix it, but if you don't have any pace, you can't do anything," Whincup said.
"We've come here with a fresh sheet of paper and we didn't really look at last year's results because they were so bad.
"But if that's our highlight [practice], then we're in for a tough weekend and we need to do something - we just need to work out what it is."
Meanwhile on the other side of the garage, Craig Lowndes was positive about making inroads with the #888 after finishing 10th in the second practice session. Lowndes has put in a strong showing across the last two rounds, and a seemingly brilliant transition to working with engineer Grant McPherson for 2015.
"It didn't go too bad today," Lowndes said.
"I think we had good balance on our used tyres. When we put our new tyres on it sort of imbalanced the car a little bit. We're struggling with a lack of front tyre grip, which is what you need around here for a good lap time, so we've got something to work at."
Lowndes believed they gathered enough useful information to prepare his car well for tomorrow, as he looks to earn his 100th race win and become the driver with the most wins at the Winton circuit - he is currently tied on four wins with Whincup, Garth Tander and Jason Bright,
"I think the beauty about today is that we know where we are now in relation to everyone else in car speed with the tyre life that we've got," he said.
"I'm not too disappointed, the car was flowing really well and Grant and I have made a number of changes. We'll sit down tonight and prepare for tomorrow, but I'm still confident that we can make a decent car out of what we've done."