The outspoken Australian had called for a medical time out at 3-2 in the first set of the exhibition event before winning it in a tiebreaker against his Belgian opponent and called for the trainer again at 1-1 in the second.
The world number 30 carried on briefly but opted to quit at the next changeover while trailing 3-2.
"Hate withdrawing, so sorry to everyone @KooyongClassic," Kyrgios posted on Twitter.
"I just have to make sure I'm right for next week & I will be."
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Kooyang Classic tournament physiotherapist Rob Hanna said the Australian had a soft tissue inflammation and that he would be fine with rest and ice packs.
"It was there a little bit this morning when he hit up before the match," Hanna was quoted as saying by Australian Associated Press.
"He got to 2-3 in the first set and said he noticed it a bit more and that's why he called me out."
Kyrgios, 20, is in good form, having helped Australia win the mixed-team Hopman Cup event in Perth last week, where he beat British world number two Andy Murray.
The Australian Open, the first grand slam of the year, begins in Melbourne on Monday with Kyrgios aiming to improve on his quarter-final appearance last year.
(Writing by Patrick Johnston in Singapore; Editing by Sudipto Ganguly/John O'Brien)
