The world number 13 went under the knife in October and has not played since his third-round exit at the US Open in August.
Nishikori was due to represent Japan in the ATP Cup in Perth but follows Yoshihito Nishioka in withdrawing from the team.
“Unfortunately I have to pull out of the ATP Cup and the Aussie Open,” Nishikori said in a statement on his 30th birthday.
“Today, together with my team, we have made this decision as I am still not 100 per cent ready/healthy to compete at the highest level.
“This decision was not taken lightly as Australia is one of my favourite places to compete. Together with my team I will keep working hard to be back on court as soon as possible. Thanks for all the support.”
Nishikori reached the Australian Open quarter-finals for the fourth time in 2019 after winning the Brisbane International.
The former world number four and 2014 US Open runner-up also recorded quarter-final appearances at the French Open and Wimbledon this year.
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