"They should and will work together," Choudhury told PTI here today.
"We cannot always pass through a smooth path, there are times when one has to face thorns, but solutions are there to get things back to normal," he said.
Choudhury termed as "unfortunate" the spat between Ganguly and Chappell but said the duo would sort out their "difference of opinion and move ahead".
"Things should not have been made public but now everything has been set right," he said.
Choudhury also said there were no problems related to discipline during the tour.
"The body language of the skipper was very good. All the team members were a disciplined lot," he said.
Choudhury, also the state's DIG, was of the view that selection matters should rest with the selection committee.
"Once the selection committee announces a team, it should be respected by all," said Choudhury, who himself had been in an embarrassing position after Jharkhand government asked him to join his duties days before the Zimbabwe tour ended.
Choudhury refused to comment on his recall saying the matter was of state government's.
The government had asked him to return since his leave was not sanctioned.