The BCCI said that it could not take on the responsibility of hosting the tournament as it would clash with the "very important" one-day series at home against Australia.
The issue will now pass to the ICC Board, which is meeting here today.
"We have said that the Champions Trophy in October will not be possible for us since we are hosting Australia at that time," Niranjan Shah, the BCCI secretary, told Cricinfo.
"The one-day series against Australia is a very important fixture for us. It has been scheduled and we can''t do anything about it. All the boards will have to find another solution or window for the Champions Trophy," he added.
The BCCI is planning to hold the first of the seven one-day matches against Australia on October 13, three days after the conclusion of the Champions Twenty20 League, which it is organising along with Cricket Australia and Cricket South Africa (CSA).
The ICC board had, on August 24, decided to postpone the Champions Trophy that was originally scheduled to be held in Pakistan from September 12 after five of the eight participating nations expressed security concerns about the host country.
David Morgan, the ICC president, said: "It was considered prudent to postpone the event to October 2009, a time when we all hope conditions may be more acceptable for all the competing teams".
The concept of an alternative structure to bilateral tours, including an enhanced Test championship, with the ICC taking a greater central "ownership" of the programme, was also discussed at Wednesday''s meeting.
However, sources said it did not appear to make much headway during the CEC meeting with a number of boards unconvinced about the idea, especially about the extent of their ownership and role under such an arrangement.
The concept was kicked off during the ICC annual conference in Dubai in July, and Cricket Australia was entrusted with the job of coming up with a plan.
The key considerations were: all three formats of international cricket should be protected and promoted with Test cricket identified as the pinnacle of the sport; "icon" Test series must be protected; ICC should look at ways of taking greater central "ownership" of international cricket outside its events or at least providing for more consistency in marketing/promotion; and the concept of a Test Championship and/or play-off should be explored further.