Cavalier King Charles Spaniels are among the affected breeds
The Kennel Club is lodging a complaint with TV regulator Ofcom about a BBC documentary exposing genetic illnesses in pedigree dogs.
The club, which runs Crufts dog show, said it was unfairly edited and did not properly reflect its "deep commitment to the health and welfare of dogs".
It also said it was reviewing its contract with the BBC to broadcast the famous show.
A spokesman for BBC Documentaries said it stood by the programme's content.
In a separate statement, the corporation said it was "seeking reassurance, on behalf of its viewers, that the objectives, practices and organisation of the breed competitions at Crufts have as a first priority the health and welfare of all dogs taking part in the competition".
An advisory panel would be set up to consider "what measures the Kennel Club should be expected to take now and commit to in the future".
It added: "The panel will be asked to give the BBC their advice quickly to enable the BBC to discuss the issues with the Kennel Club before planning begins for coverage of Crufts 2009."
Crufts has been transmitted on BBC Two since 1966.
The move comes after the RSPCA pulled out of the show over welfare concerns.
Clips from the BBC documentary about pedigree dog breeding
Pedigree Dogs Exposed, which aired last month, said physical traits required by the Kennel Club's breed standards, such as short faces and dwarfism, lead to inherent health problems.
The deliberate mating of close relatives, in particular, had left animals suffering from epilepsy, breathing problems and deformities, it claimed.
The documentary also said dogs suffering from such conditions were not prevented from competing in dog shows and had gone on to win "best in breed", despite their poor health.
Kennel Club spokeswoman Caroline Kisko told the BBC it was not "a tenable position" for the broadcaster to show Crufts - a programme "celebrating dogs" - when it had also aired a documentary "which was clearly so heavily biased against dogs".
"All of those dogs that were shown on the programme were taken to be to do with the Kennel Club," she said.
"The message put across by the programme was that all their disabilities, their illnesses, were caused by something which the Kennel Club had done, to the point where we were likened to Nazis."
Ms Kisko said the Kennel Club had recognised that "things had gone too far" with some breeds several years ago and was making efforts to address their health issues.
But she added: "The fact of the matter is that the large majority of pedigree dogs in the country are healthy."
In a separate interview, Ms Kisko told the BBC the Kennel Club currently allowed inbred dogs to be registered with them - a requirement for entry into Crufts.
But that position would be reviewed in the next few months following the expected publication of research, by scientists at Imperial College, into whether inbreeding had detrimental effects, she added.
A second charity, Dogs Trust, has also announced that it is withdrawing from Crufts and the Westminster Dog Show.
In a statement, it said: "Dogs Trust believes that this removal of support is the strongest signal it can give to the Kennel Club and breeders to achieve immediate action to ensure that the health and wellbeing of pedigree dogs is ranked over appearance and artificial breed standards."
Crufts' sponsor, and dog food maker, Pedigree said it was "concerned at the findings of the BBC's recent documentary".
"Pet health and welfare is our primary concern at Pedigree and we are committed to continuing our work with all parties to promote responsible dog ownership."
The RSPCA is carrying out a scientific review of pedigree dogs and their care which will be released in January.
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