Thousands of junior doctors have marched in London and Glasgow in protest at medical training reforms.
Ministers have already agreed to review the online system
They claim their careers are being held back by a "badly-organised" online application system and too few specialist jobs to apply for.
Addressing the London protest, Tory leader David Cameron said the online system was an "utter shambles".
Health Minister Lord Hunt admitted there had been "teething problems" with the system but promised to fix them.
The online questionnaire-based application, called Medical Training Application Service (MTAS), was designed to speed up the process for placing junior doctors in specialist jobs.
But a catalogue of complaints has emerged.
Doctors say the forms are badly worded, do not ask pertinent questions, do not allow them to set out relevant qualifications and experience, and have no facility for attaching a CV.
The result, they say, is that the best candidates are not being selected for the right jobs.
Andrew Rowland, vice-chairman of the British Medical Association's junior doctors' committee, said the whole system, which the applications are part of, was an "absolute disaster" and called for an independent review.
"We need this system to be halted until we can find out exactly what went wrong and to make sure that can be corrected."
At the Glasgow protest Dr Rowland's Scottish counterpart, Dr Graeme Eunson, called for Health Secretary Patricia Hewitt to resign.
The protesters, organised by campaign group Remedy UK, are also aggrieved that about 28,000 UK trainees are applying for 22,000 posts.
Mr Cameron said the application system should be scrapped if the government could not address concerns.
And he said there should be a specialist post for "every junior doctor in England".
He said the Conservatives would treat doctors like "human beings", and pledged to hold the government to account.
The Department of Health has already said there will be "significant" changes to the system before the second round of interviews for specialist posts - due to begin in April.
The changes will include allowing applicants to provide CVs and portfolios to support their applications.
Those who have not been short-listed for interview will have a one-to-one assessment before being recommended for an interview stream.
And the most experienced juniors applying for jobs, who are likely to have taken time out to complete a PhD, will be guaranteed an interview for their first or second choice places. Lord Hunt insisted that the government wanted "the best doctors to get into those specialty training posts".
"I want to assure junior doctors that we are doing everything we can to sort the issues that they've raised out," he said.
Doctors' training was revamped in 2005, with the aim of speeding up progress so juniors could reach consultant level in an average of 11 years, rather than the current 14.
However doctors who have been through their initial stage of training under both the old and the new systems are all competing for a limited number of specialist training posts.
This is the point at which a doctor would select to focus on an area such as cancer medicine or paediatrics.