BCCI President Shashank Manohar was forced to interfere to sort out the issue, the report said.
The newly formed selection committee, headed by former Indian cricketer Kris Srikkanth had met on Wednesday for the team selections when the differences apparently cropped up.
Last year, Rahul Dravid too had relinquished captaincy. Lack of say in selection matters was widely touted as the reason behind Dravid"s abrupt decision.
All-rounder Irfan Pathan had made the cut in place of RP Singh who had dished out mediocre performances in opening 3 ODIs.
The BCCI, however, was quick to rubbish the reports. "I cant respond to something that is being floated around by somebody", BCCI secretary N Srinivisan said.
Senior BCCI official Rajiv Shukla also said the reports were not true.
"The reports are baseless and we cannot comment on such reports. There were no differences between the selectors and Dhoni", Shukla said.