Ministers have been urged to tighten up access to the NHS database, amid concerns details are being seen by NHS staff without medical qualifications.
The scheme is aimed at modernising the NHS
News that healthcare assistants are getting access to patients' records "drives a coach and horses" through assurances on security, doctors say.
The NHS says they have access only to basic details including allergies and medication, not full medical histories.
It follows a Computer Weekly report on pilot trials of the new database.
The plan to put 50 million patients' records on the database is part of a controversial £12bn NHS IT overhaul, but has been criticised for its cost and the security risks.
Freedom of Information requests by Computer Weekly suggest that patient's confidential records have been accessible to healthcare assistants during pilot trials of the new database.
Paul Cundy, of the British Medical Association's IT committee, told BBC Radio 4's Today programme that "breaches all common concepts of privacy and confidentiality".
He said when the database was planned, the BMA had sought assurances and had been told there would be "role-based access control", allowing GPs to see entire records, but more junior staff to see only names, addresses and telephone numbers.
"The practice, it transpires, is that healthcare assistants - who are nothing other than trained receptionists or telephonists - actually are being given access to the clinical records," he said.
"It drives a coach and horses through the assurances we were given about role-based access control."
Dr Cundy added that he had opted out of having his own details put on the national database - as all NHS patients are entitled to do - but said the BMA was not giving blanket advice for everyone to do so.
But a spokeswoman for NHS Connecting for Health, the government agency running the database project, said the Computer Weekly story was "misleading".
She said the records concerned were "summary care records", which contain basic details such as a patient's name, address, telephone number and any allergies or current medication.
"We are in the very early stages of introducing what will be a very important trial in terms of providing safe out of hours emergency care," she said.
She added that an earlier proposal to allow receptionists access to the details had been dropped, as doctors had said only medical staff should get access, but said healthcare assistants "are very much part of the team that is involved with the care of patients". They would have access so they could help A&E clinicians.
The scheme has raised concerns over cost and the security of information. A poll of more than 1,000 doctors for the Guardian last November suggested that 59% of GPs in England were unwilling to upload any record onto the database without the patient's specific consent.
The database is part of plans to modernise the NHS and represents the largest single investment in IT in the UK.
By 2014, 30,000 GPs in England will be linked up to nearly 300 hospitals giving the NHS a "21st Century" computer network.
It involves an online booking system, Choose and Book, a centralised medical records system, e-prescriptions and fast computer network links between NHS organisations.