The injury, similar to the one suffered by star batsman Sachin Tendulkar, may force Ganguly to skip a major domestic tournament next week which is a selection trial for the upcoming one-day series against Sri Lanka from October 25.
Ganguly was due to lead Indian Seniors in the three-team Challenger one-day series in Mohali from October 10-13.
"It is uncertain whether he will actually play," the Times of India said on Tuesday. "He is yet to confirm his participation, and obvisouly, the tennis elbow -- if it is that at all -- is to blame."
The injury came at the wrong time for Ganguly, struggling to retain the captaincy as well as his place in the side.
Tendulkar missed tours of Sri Lanka and Zimbabwe and the International Cricket Council's Super Series in Australia after a surgery on his left elbow in May. He has, however, been declared fit to play the Mohali tournament.
Ganguly has been in the eye of storm because of his dipping form and spat with coach Greg Chappell.
The Indian captain claimed on the recent tour of Zimbabwe that he had been asked to step down by the coach.
Their relationship soured when Chappell said in an e-mail to the Indian board that the captain was unfit the lead the side, forcing the cricketing chiefs to broker a truce between the two.
It appears to be a temporary respite for the captain, who is under pressure to prove his form.
Indian cricket chief Ranbir Singh Mahendra said the selectors would take "appropriate" action if Ganguly's performance did not improve.
"I hope his return to form happens soon and he fulfils the expectations, but the final decision about his future will be of the selection committee," Mahendra said in a recent interview.
"I agree Sourav Ganguly is not in good form these days, but it cannot be ignored that he scored a century recently."
Mahendra was referring to Ganguly's painstaking six-hour hundred against Zimbabwe in Bulawayo, the captain's first three-figure knock since November 2003.
The century still failed to silence Ganguly's baiters as it came against the weakest attack in international cricket.
Former England captain Nasser Hussain, meanwhile, hinted that Ganguly should not be captain if he did not find batting form.
"Then only he can question any player not scoring runs on his face," said Hussain, who was in Mumbai on a private visit.
"You can get the team to do anything for you, but it should never come to a point where a player can turn around and ask you, 'Are you getting any runs yourself'.
"After all this battle, I don't know whether Sourav has got the mental energy to get India to the number one position which they deserve to reach."