Halep, whose career has stalled due to a doping ban that was reduced on appeal this year, received a wildcard for the Aussie Open qualifying tournament last week.
But she posted on social media on Thursday that she was suffering pain after participating in an exhibition event in Abu Dhabi.
The 33-year-old was runner-up to Caroline Wozniacki at the Melbourne major in 2018.
The two-time Grand Slam champion had also been scheduled to play at a tune-up tournament in Auckland.
Halep last played at the World Tennis League exhibition event in Abu Dhabi last week.
"After playing in Abu Dhabi, unfortunately I felt pain in my knee and shoulder once again. After discussing with my team at length, we agreed it is sensible to delay the start of my season," Halep wrote on Instagram.
"It's not what I wanted but I would like to thank the tournament organisers in Auckland and Australia for the wild cards and I'm sorry I won't be able to take them this time."
The Romanian said she is planning to next enter the Transylvania Open in Cluj in her home country, where play begins February 3.
Halep was provisionally suspended in October 2022 after she tested positive for roxadustat - a banned drug that stimulates the production of red blood cells - at the US Open that year.
She was later banned for four years, a period which was cut to nine months in March following an appeal at the Court of Arbitration for Sport.
The 2019 Wimbledon champion has denied knowingly taking roxadustat, blaming contaminated supplements for her positive test.
Australian Open qualifying starts on January 6, with the main draw beginning on January 12.
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