Hamilton, who damaged his car's floor on a low fuel run that then hampered his long run effort, was only 11th in the second session.
"The car's a bit of a struggle today. It's crazy how much it swings from track to track," the Briton, who was second in France last weekend and is a record eight times winner in Hungary, told Formula One television.
"At the moment it's a little bit loose and it's not doing what we want it to do. Difficult day ... it’s going to be a tough weekend, that’s for sure."
Mercedes said they had redesigned the profile of the Halo head protection device and made changes to the rear wing.
The reigning champions have yet to win in 12 races this season but have sounded hopeful of closing the gap to leaders Red Bull and Ferrari, with the latter team top in both sessions on Friday.
"We came in wanting to do some experiments with the car and I think the ones we did in FP2 with both (drivers) have taken us backwards," trackside engineering director Andrew Shovlin told Sky Sports television.
"In the first session we looked a bit stronger, the car was more together. There's a couple of things I'm pretty certain we're going to be undoing overnight because it didn't look great.
"I think some of the setup changes we’ve gone the wrong way. We’re here to learn, you don’t always get them making the car go quicker."
The forecast for qualifying at the Hungaroring is rain, with temperatures also dropping for Sunday's race compared to Friday's hot conditions.
"The conditions on Sunday are going to be drastically different so we were trying quite a few things with the car, using it as a bit of a test session," said Hamilton's team mate George Russell.
"You can try and optimise everything for today but there is no use of that at all for the rest of the weekend. So, even though it was a very tough day, I think it was a productive one."
