Federer returned from an injury lay-off in 2016 to win the Australian Open earlier this year in what was his first Grand Slam victory since 2012.
The Swiss superstar went on to win additional six titles, including a record-breaking eighth Wimbledon crown as he currently sits at number two in the ATP tennis rankings.
Now set to defend his title in Melbourne in January, Federer faces a tougher task as the first Grand Slam of the year will see the returns of many stars making their injury comebacks.
Having dropped in the rankings as a result of their absences in 2017, the seedings for the event will lead to earlier match-ups between the top players, and Hewitt believes there will be question marks over the returnees.
"Coming in a lot of the top guys from the previous years are gonna be seeded a lot lower," Hewitt said, as quoted on Tennis World USA. "Such as Djokovic, Murray...that kind of guys — just because they haven't played really for the last six months.
"So, it's gonna be a massive question mark on how they come in, how their bodies are holding up. Mentally as well with a couple of them."
Regardless, the Australian believes Federer will still go into the event as the favourite, especially considering world number one Nadal had to pull out of the ATP Finals in London with a knee problem.
"But also, you know, Federer has been so dominant, especially in big tournaments," Hewitt added.
"He's gonna go in — even at the age of 36 — as probably the favourite. Especially the way Nadal obviously had to pull out of London."
The 2018 Australian Open will take place from 15–28 January.