Studio co-president Christophe Balestra told Edge Magazine that 2009's Uncharted 2: Among Thieves was so ambitious that the team was almost unable to make it run on the PlayStation 3 hardware.
He explained that the award-winning title wouldn't fit in the console's memory three weeks before its shipping date, though a solution was found later.
However, Mr Balestra assured gamers that these difficulties have not curbed Naughty Dog's ambitions for Uncharted 3, saying the developer is once again looking to go "beyond" the limits of the powerful hardware.
"We're driven by artists and it's the job of the programmers to make it fit, in terms of memory and frame-rate," he said.
Uncharted 3: Drake's Deception launches at the end of the year and will relocate the action to the vast Arabian Desert, as well as introducing stereoscopic 3D graphics to the series.