Harbhajan, 28, suffered a toe injury during the second Test in Mohali which India won by 320 runs to go 1-0 up in the four-match Border-Gavaskar series. The first Test in Bangalore ended in a draw.
"We are not sure about Harbhajan," Kirsten told reporters on Monday.
"He picked the injury towards the end of the last game. It is probably because of overuse. We will have to wait and see how he goes. We will assess his condition again tomorrow. There are still 48 hours for the match."
The wily spinner, with eight wickets in the first two Tests, has troubled the Australian batsmen with his nagging line and length.
Harbhajan was instrumental in India winning the 2001 home series against Australia when he picked 32 wickets from three Tests, including a hat-trick at Kolkata.
Kotla specialist Kumble 'fit' for Delhi Test
Kirsten also said that promising leg-spinner Amit Mishra would sit out of the Delhi Test if captain Anil Kumble recovered from a shoulder injury.
Mishra played the previous match as a last-minute replacement for Kumble, a leg-spin veteran of 131 Tests, and picked seven wickets on debut.
"If Kumble is fit, he will take Mishra's place. Kumble is looking good at the moment and we are very happy with the way things have been progressing for us," said Kirsten.
Australia were also sweating over the fitness of paceman Stuart Clark, who missed the last Test due to a sore elbow.
"We spoke to the physio about Stuey. He is looking good for the game, but we will wait before making any final decision on him," Australia vice captain Michael Clarke said.
Clark took just one wicket in Bangalore, but did a good job of containing the Indian batsmen, giving away 70 runs from 28 overs.