Dolgopolov, seeded 21, was due to face Italian Paolo Lorenzi in the first round of the Aus Open but may have suffered a torn meniscus.
He will undergo an MRI scan later on Friday.
In the first set tie-break against Fernando Verdasco in the Kooyong Classic final earlier on Friday Dolgopolov started to clutch at his knee.
He called for a trainer before retiring, handing Verdasco the title.
The Ukrainian told media afterwards that the injury felt the same as the knee injury in July that sidelined him for 10-weeks after surgery.
"When I was warming up and playing the first set it was fine and the last few games I started feeling something strange in the knee and it started to get worse," he said.
"I'm not sure I'll be playing in the Open because it feels quite the same like I did before the surgery.
"My physio is saying 99 per cent meniscus that I injured before," he added.