The coach-captain spat worsened Friday when Chappell reportedly said in an e-mail sent to the Board of Control for Cricket in India (BCCI) that he believed Ganguly was no longer fit to lead the side.
Chappell, the former Australian Test captain and batting great who took charge of the Indian team in June, was also said to have threatened to quit if the captain was not changed.
"I don't think the entire team should be dragged into this," Ganguly said on the team's return from Zimbabwe where his side won 2-0 to post their first Test series win outside the sub-continent since 1986.
"It was some statement made by the coach," the Indian captain said. "It is between the coach and me and we have to sort it out."
"I do not think the rest of the boys need to be pulled into this. For us, it was important winning the two Tests and we won them convincingly."
Relations between Chappell and Ganguly soured ahead of the first Test in Bulawayo when it was revealed the coach had asked the captain to step down because of his poor batting form.
Ganguly responded by scoring a painstaking six-hour century against the weakest attack in cricket and then revealed the dressing-room discussion with the coach to the media.
The Indian captain declined to comment on the coach's e-mail, saying it was a "sensitive issue".
"I do not want to talk about this issue," he said.
"Yes, I am aware of it (the e-mail). I will talk to the Board on the issue if they ask me. It is a sensitive issue at the present moment and I do not want to say anything to stir it up again."
The coach reportedly said in the e-mail he believed Ganguly was not "physically or mentally" fit to lead the side.
"Chappell has told the Indian board that he will find it difficult to continue if Ganguly is retained as captain," a board source, who has seen the e-mail from Zimbabwe, told AFP on Friday.
"The coach believes Ganguly is not physically or mentally fit to lead and had lost the respect of the younger players in the team," the source said, speaking on condition of anonymity.
The board will discuss the row at a meeting here on Tuesday.
Ganguly said it was important for the team to perform well in coming months and it did not matter who the captain or coach was.
"It is important that the team does well regardless of whoever leads it or coaches it. The team is more important than individuals," he said.
"We need to play good, hard cricket as we will be facing very good teams. We will be playing Sri Lanka at home, then tour Pakistan and play England at home before going to the West Indies.
"It is going to be tough and we need to get our act together."
Ganguly conceded his team had yet to find a formula for winning One-day finals.
"To be honest, we have not been able to find the solution of how to win the finals. We understand it is getting difficult after losing so many finals in a row."
India have lost more than a dozen finals in recent years, including two this season against Sri Lanka in Colombo and New Zealand in Harare.