Two of the three venues selected by the ICC, the Ferozeshah Kotla in New Delhi and the Wankhede stadium in Mumbai - backed out citing prior sponsorship commitments and reluctance to part with clubhouse tickets.
The third venue, the Eden Gardens in Kolkata, wants to host only the semi-finals and final in November because of the threat of wet weather in the eastern metropolis in October.
The monsoons have also ruled out hosting matches in Bangalore and Chennai, the two other major cricket centres in the country.
"We are struggling to give three suitable venues to the ICC for the tournament," Indian cricket board secretary Niranjan Shah told AFP on Thursday.
The event, organised by the ICC every two years to raise funds for the promotion and development of the game worldwide, is scheduled to be held in India between October 7 and November 5.
The tournament, regarded as a mini World Cup, features the top six limited-overs nations plus two qualifiers drawn from the remaining five teams with official One-day international status.
The stadiums in New Delhi and Mumbai have prior commitments for providing on-ground advertising and tickets to their sponsors which conflict with the ICC's diktat that it needed sole control of each venue.
"We have our own commitments. We just can't hand the entire stadium to the ICC," said Delhi cricket official Sunil Dev.
The ICC's commercial partner, the Global Cricket Corporation (GCC), is scouting for suitable venues across India, but with little success.
The GCC ruled out the Rajiv Gandhi stadium in Hyderabad because it was still incomplete and also rejected the Vidarbha Cricket Association ground in Nagpur because of insufficient hotel rooms in the city.
The Sawai Man Singh stadium in Jaipur was approved, but the local cricket association said it did not want to host the tournament.
The Punjab Cricket Association stadium in northern Mohali, one of the finest Test venues in India, also has prior sponsorship and ticketing commitments.
The GCC has zeroed in on the Cricket Club of India (CCI) in Mumbai, which last hosted a Test match in 1972 but has organised One-day internationals in recent years.
India is a reluctant host with officials saying over the past few months that the tournament needed to be scrapped because it diluted the importance of the four-yearly World Cup and caused huge financial losses to the host country.
"We will honour our commitment to organise the Champions Trophy this year but want the tournament to be taken off the calendar in future," an Indian official had told AFP in December.
"Since the ICC takes away a major part of the revenue, the tournament is a financial burden on the country which hosts it."
The Champions Trophy was the brainchild of former Indian and ICC chief Jagmohan Dalmiya, who lost control of the Indian cricket board in November when his faction was voted out by political heavyweight Sharad Pawar.
The previous four editions of the Champions Trophy were hosted by Bangladesh (1998), Kenya (2000), Sri Lanka (2002) and England (2004).