The South Americans beat Poland 2-0 on Wednesday night to top their group and set up Saturday's knockout clash.
"I think it's absolute madness to play in nearly two days and a bit when we are top of the group. I can't understand it," Scaloni said, talking to the media after the game at Doha's 974 Stadium ended just before midnight.
"What time is it? Nearly one o'clock in the morning ... Thursday, the next day is for preparation and then we play. Those aren't good conditions but it's the same for everyone. We're first in the group. We could have had more rest."
Australia will only benefit from a few hours' more time to recuperate and prepare than Argentina, given their last group match was completed earlier on Wednesday.
But Scaloni's comments touch on the wider controversy over holding the World Cup in Qatar due to the hot conditions and more compressed timetable.
Argentina have found their rhythm again in beating both Mexico and Poland comfortably in Group C after their shocking opening loss to Saudi Arabia. But Scaloni said they must be wary of Australia who fought their way to the last 16 with gritty wins over Denmark and Tunisia.
"Our fans should enjoy this. We are happy today but we don't want to be euphoric," he said.
"All the games are hard. Anyone who thinks the match against Australia will be easy is wrong. We're not favourites. If you think that just because we won today, we are going to become World Cup winners, you're wrong."
Scaloni said he took striker Angel Di Maria off in the second half to protect him. "Di Maria had some discomfort in his quadriceps and we decided to substitute him. If there's a chance that he gets injured then it's not worth it," he said.
He praised his team for neutralising Poland's counter-attacks and keeping attacker Robert Lewandowski quiet.
"We didn't really allow them to counter-attack. It was to our credit. I think that we read the match very well. My players did a great job. They played very well and I am very happy."