Ducati has insisted that this would be a building year as it moved back towards the front following two barren seasons.
But both Hayden and new team-mate Andrea Dovizioso struggled on the first two days in Malaysia, ending day two at the foot of the top 10.
"Yesterday was two seconds off, today's a second and a half. It would be great if we could take another half a second out of it tomorrow but I don't know how easy that's going to be," Hayden told the MotoGP website.
He conceded that to fall further away from the pace was a blow to morale.
"It's still a bit frustrating to be so far away. Even further away than we ended last year, I guess," said the 2006 world champion. "It's really tough on all the guys and me."
Although Ducati did gain some pace on Wednesday, Hayden played downs any hopes of a breakthrough.
"We didn't make any huge changes," he said. "The track was a lot better today, that helped us. Any time the track is more grippy is a lot better for us, so we're thankful for that."
Hayden said Ducati would try and squeeze what more it could from its current package on the final day of the first test on Thursday.
"Tomorrow we've got a couple of little ideas that should help us," he said.
"We've got some stuff to try with electronics, driveability and a few geometry set-ups. We don't really necessarily have anything major to test, nothing really new.
"We'll just test about with the stuff we've already got and see if we can make anything any better."