Laid low with a tennis elbow, it will now be all the more difficult for him to save his captaincy as well as his place in the side, and the 33-year-old admits he has a battle on his hands.
"I just want to work harder and get fitter," he said.
"I am trying to get into shape for the season. I hope to be fit for the Sri Lanka series" which starts on October 25, he said.
Ganguly has been dogged by form and fitness problems in recent months. He contributed just 48 in three home Tests against Pakistan early this year.
He scored a century against Zimbabwe in the opening Test at Bulawayo last month, but his painstaking six-hour knock against the weakest attack in international cricket did not satisfy all his critics.
Ganguly and coach Greg Chappell were involved in a public spat last month with the coach saying in a leaked e-mail to BCCI chiefs that the captain was unfit to lead the team.
Ganguly, the most successful India captain with 21 Test victories, is only the fourth batsman in one-day cricket to complete 10,000 runs after compatriot Sachin Tendulkar, Sri Lankan Sanath Jayasuriya and Pakistan's Inzamam-ul-Haq.
The left-hander was given a chance to regain form before the upcoming one-day series against Sri Lanka when he was named captain of an India Seniors side for the October 10-13 domestic Challenger Series in Mohali, the last tournament for players to stake claims.
But he was ruled out of the tournament on Friday after being advised to rest for 10 days by doctors. His injury has given selectors a dilemma as they have to pick the captain on October 13 and the team the following day.
The selectors are unlikely to risk naming an unfit, out-of-form Ganguly.
Life has been tough with India's most successful Test captain since April, when he was banned for four matches for his team's slow over-rate against Pakistan in a home one-day series.
Five months later, he finds his runs have dried up and his body has become vulnerable.
Ganguly had been credited with transforming India into a fighting unit capable of playing competitive cricket even away from home. He had also been lauded for backing under-pressure youngsters.
He was named captain in 2000 when Indian cricket's credibility was low following a betting and match-fixing scandal. He proved his worth in testing times, leading his side to an Indian record of 21 Test wins. He has scored 5,066 runs in 84 Tests.