The 20-year-old has struggled with injuries during the past 15 months and was a late withdrawal from the Sydney International with an abdominal strain.
It is unclear whether he will play in the doubles when the Open starts at Melbourne Park on Monday.
Kokkinakis had been poised to make a long-awaited singles comeback after enduring shoulder, pectoral and groin injuries.
Tournament director Craig Tilley on Friday said Kokkinakis would be replaced by a “lucky loser” from the qualifying draw.
The ATP event at Indian Wells in March appears the next most likely tournament for Kokkinakis to re-launch his career.
Meanwhile, big home hope Nick Kyrgios – who this week pulled out of Adelaide’s World Tennis Challenge with his own injury concerns – will launch his Australian Open campaign against Portugal’s world No.81 Gastao Elias.
Former champion and world No.4 Stan Wawrinka looms as 14th-seeded Kyrgios’ first major test in the fourth round.
A quarter-finalist in 2015, Kyrgios will meet either Andreas Seppi or fellow tour veteran Paul-Henri Mathieu should his suspect knee hold up sufficiently to get past Elias.
Kyrgios could meet countryman Sam Groth in the third round before Wawrinka – the reigning US Open champion and only man in the past seven years to conquer Novak Djokovic at Melbourne Park – is likely to be lying in wait in the round of 16.
In a tough draw, Bernard Tomic – Australia’s only other men’s seed – opens his campaign against Brazilian baseliner Thomaz Bellucci and has Marin Cilic, Jo-Wilfried Tsonga and Jack Sock lurking in his section.
Australian Open wildcard playoff winner Omar Jasika has drawn Spanish 21st seed David Ferrer, while teenage wildcard Alex De Minaur meets Austrian Gerald Melzer.
World No.1 Andy Murray opens against Ilya Marchenko, while six-times winner Djokovic plays Fernando Verdasco, the Spaniard who upset Rafael Nadal in the first round last year and held five match points against Djokovic in Doha last week.
Seeded 17th in his first major since Wimbledon last year, four-time champion Roger Federer has a qualifier first up, while fellow Swiss Wawrinka plays Martin Klizan of Slovakia.
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