Ed Cowan top-scored with 44 in a shocking collapse of 8-56 which followed Australia's eight-wicket loss in the first Test in Chennai.
Cowan, his fellow opener David Warner, No.3 Phil Hughes and No.4 Shane Watson are all averaging under 30 after two matches in the series, while Clarke has made 267 runs at 67.00 including a century in Chennai batting at No.5.
Hughes has scored 25 runs at 6.25 in two matches and could be facing the axe for back-up batsman Usman Khawaja.
"I think I have no choice," an ashen-faced Clarke told his post-match media conference on Tuesday when asked about promoting himself up the order.
"Again, it hasn't been about me, it's about trying to do what's best for the team, and I think now, especially in these conditions, I have to bat higher."
Asked where in the top four he would bat, Clarke added: "I've got nine days to work it out.
"Wherever I can go and put some runs on the board to help the team."
Clarke's 1595 runs in 2012 was the fourth-highest tally in Test history for the calendar year.
The third Test starts in Mohali on March 14.
Australia can retain the Border-Gavaskar Trophy if they score victories in the third and fourth Tests.
Australia's players had been expecting to take a few days off between the second and third Tests. However this was yet to be finalised on Tuesday as squad members including the out-of-form Hughes returned to the field for centre-wicket training.
TV commentator Matthew Hayden, who tamed India's spin attack in 2001, mingled with the players during their post-match session.
Australia's second-innings total of 131 is their lowest score in a Test in India since making 93 in Mumbai in 2004.
Clarke said he was more concerned with Australia's first-innings performances of 380 and 9-237.
"We won both tosses and the wicket has been at its best both times to bat and 237 is unacceptable," he said.
The skipper says the solution is hard work in the nets.
"I know you don't get better as a player by sitting on the couch and doing nothing," he said.
"We're fortunate in regards to having eight or nine days before the third Test."
Clarke said he couldn't say if Tuesday's loss was his worst or most painful as captain.
"Who knows. They're always tough when you lose," he said.
"They're even tougher when you perform like that."
Clarke is confident there's enough talent in his batting line-up to score big totals but he has admitted the criticisms from the Indian camp about a lack of patience have been on the money.
"Our shot selection has been horrible," he said.
A team spokesman later announced coach Mickey Arthur planned to hold a training session in Hyderabad on Wednesday followed by a three-day break for the squad.
- AAP
