Forensic medical examiners are refusing to sign a new contract with the Metropolitan Police (Met) over fears they will lose their independence.
Half of the FMEs, who can be involved in rape and terrorism inquiries, have refused to sign the agreement.
They argue the contract could undermine patient-physician confidentiality and say the dispute puts detainees at risk.
The Met said the row would not affect the quality of the service and that it would outsource to fill any gaps.
Under the new contract FMEs would have to conform to any new records policy introduced by the Met, which may require FME's to divulge patient information.
Private information
Dr Robin Moffat, President of the Medico-Legal Society, expressed concern that the contract would affect the confidentiality relationship between patient and physician.
He said: "I don't think it is going to be helpful to allow police forces to have access to personal, private information. It is against all rules of confidentiality between physicians and patients. "
Dr Michael Wilks, the chairman of the Society of Forensic Physicians, said it was vital FMEs were seen as impartial as part of the role involves giving evidence in court.
"There is absolutely no crisis at all. We have 24/7 forensic medical cover in all of our custody suite in London"
Speaking after negotiations with the Met over the matter he said: "The situation is extremely serious.
"This is a specialised area of care which requires experience and training. We are unconvinced that the Metropolitan Police Service can find enough doctors with the right competence to provide a safe service as well as one that preserves the integrity of the forensic service."
He said the current system was being "thrown away" in favour of "a totally untested, probably unsafe and unqualified service".
BBC London News has obtained a letter sent confidentially to all borough commanders which stated there will "rare occasions that the outsource company are unable to fill a particular shift."
The letter states consideration "will need to be given to removing the person to hospital".
Meanwhile Det Supt David Imroth said: "We are entirely comfortable that the outsource company we are going to utilise to fill the gaps in the short term are only employing entirely appropriately trained doctors, specialist doctors who will be able to maintain the same levels of service provision we currently enjoy.
"It is far from a crisis. There is absolutely no crisis at all. We have 24/7 forensic medical cover in all of our custody suite in London."
"No custody suite will be closed. The service will be continued uninterrupted."
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