Sebastien Loeb still leads the way from both Mikko Hirvonen and Jari-Matti Latvala, who are tied 29.4 seconds behind the Frenchman.
Atkinson is two minutes 42.1 seconds in arrears of Loeb, over a minute behind the fifth-placed Daniel Sordo but nearly two minutes clear of Henning Solberg who is seventh.
Tomorrow Atkinson will seek to bring his Impreza WRC2007 home safely and add points to his season's tally, but day two on the island of Sardinia was a matter of survival.
Atkinson started the day in fifth place but by the second stage was back in sixth, where he remained across the remaining four special stages of Leg Two.
The Queenslander's fellow Subaru World Rally Team (SWRT) driver, Petter Solberg, also had a difficult day, starting out in third place but finishing tenth, his problems compounded by a puncture on Special Stage 8.
The team explained that the unusually cool conditions being experienced on Sardinia caused real issues for the drivers.
The Impreza WRC2007 is remarkably light on its tyres; a virtue normally much sought after in the hotter rallies where tyre wear can be crippling. But today, in the slippery conditions, it actually became difficult to generate sufficient heat in the hard compound Pirelli tyres for them to realise their full grip.
The very nature of the island stages exacerbated the issue as Atkinson and Solberg could ill-afford to slide their Imprezas excessively through the narrow and rock-strewn routes.
"We seemed to face a new challenge of getting heat into the tyres in the cold conditions we faced today," said team boss, David Richards.
"Both drivers did a very good job under difficult circumstances, but it is clear that we haven’t got everything working correctly in these temperatures."
For his part, Atkinson knew he had done all that he could.
"We’ve still been pushing hard today," Atkinson said. "We knew the Fords (Hirvonen, Latvala and Galli) would be quick, so it's no surprise to be sixth.
"I felt I drove well today, and that is all I can do. I drove the best I could and pushed as hard as I could, and I made no mistakes and we didn't have any problems, so that is good.
"We're still in a good position, but we just didn't have the pace to stay with the front guys."
The SWRT crew will make changes to the Impreza WRC2007s for tomorrow's final five stages to try and address the tyre temperature problem.
The final day of this fifth WRC event in Sardinia takes crews through four new stages to the south of the service park, which whilst a change from previous years use a combination of familiar roads.
The event's finale is a 2.7 kilometre spectator stage that skirts the beach to the north of Olbia in the Costa Smeralda region. The five stages comprise a total competitive distance of just fewer than 80 kilometres.
Results after day two – Rally Italia
1. Loeb / Elena, Citroen C4 WRC, 2h 59m 21.5s
2. Latvala / Anttila, Ford Focus RS WRC 07, +29.4s (diff. to 1st)
= Hirvonen / Lehtinen, Ford Focus RS WRC 07, +29.4s
4. Galli / Bernacchini, Ford Focus RS WRC 07, +1m 17.7s
5. Sordo / Marti, Citroen C4 WRC, +1m 31.3s
6. Atkinson / Prévot, Subaru Impreza WRC2007, +2m 42.1s
7. Solberg / Menkerud, Ford Focus RS WRC 07, +4m 29.0s
8. Aava / Sikk, Citroen C4, +4m 34.5s
9. Andersson / Andersson, Suzuki SX4, +5m 45.9s
10. Solberg / Mills, Subaru Impreza WRC2007, +7m 29.2s
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