"There is no doubt about it because you didn't have (David) Warner, (Josh) Hazlewood and (Mitchell) Johnson, so there's three players straight away you'd imagine would come back into the reckoning for the first Test.
"And also different conditions, you're not going to have two spinners at the Gabba in the first Test."
Uncapped Tasmania paceman Fekete is likely to be one of the casualties despite taking 4-30 against Queensland on Monday.
"There's going to be some guys picked for that tour who are probably going to get shuffled back down the order a little bit, but you can't do anything about it," Waugh said.
"He (Fekete) is certainly not out of the equation of playing Test cricket in Australia, particularly with fast bowlers, they tend to get injuries, and he's around the mark that's for sure."
Waugh believed the loss of the two-Test tour of Bangladesh would not have a major impact on preparation for the New Zealand series and the rest of the international summer.
It meant Australia's representatives have the rare opportunity to play three weeks of domestic one-day cricket in the Matador Cup.
They will then feature in just a single first-class match prior to the first Test against the Kiwis.
"You don't have a lot of red-ball cricket, but there's still a lot of cricket to be played," said Waugh.
"Whether that's better than going to Bangladesh in foreign conditions, and whether that's a better warm-up is perhaps questionable.
"But players are used to swapping and changing formats, so whilst it's probably not ideal we didn't play the two Tests in Bangladesh it also gives a chance for some players to freshen up."
-AAP