About 200 junior doctors have held a rally in Glasgow in protest at the recruitment process for specialist training posts.
Junior doctors say the new selection process is flawed
Doctors said the new UK-wide training arrangements had left some of the brightest students with no post.
The Modernising Medical Careers (MMC) procedure is already under review.
Following pressure from doctors, the MMC website announced that all eligible applicants would now be given face-to-face interviews.
However, that means thousands of interviews must take place before the successful candidates are due to start work in August.
The problems began when the way junior doctors are selected for their first training places in a specialty changed for the first time in more than a decade this year.
It was intended to introduce a fairer selection process and speed up the amount of time doctors spend in training before becoming fully qualified.
Independent MSP Dr Jean Turner spoke at the rally
However, many going through the first round of interviews were unhappy.
They said a new computerised application system did not allow candidates to show a range of experience and that some of the best candidates have therefore not been selected for interview.
The junior doctors calling for reform of the system gathered in George Square in Glasgow and St Andrew's Place in London on Saturday.
Dr Kevin Cormack of Remedy UK, a group representing doctors who have lost confidence in the new training system, said: "There's a computerised training system that's basically gone disastrously wronging selecting doctors for the right jobs."
He said there has been about 30,000 applications for about 22,000 posts.
Scotland's chief medical officer Dr Harry Burns: "It is currently planned that junior doctors who are unsuccessful at being short-listed in the first round will be offered appropriate advice and expertise (by NHS Education for Scotland) to help with future career planning for Round 2 of applications, which is due to start in April.
"These plans may change in light of advice from the review group being chaired by Neil Douglas.
"Suggestions that thousands of doctors will be left with no jobs to go to are completely false."
He said Scotland would have at least the same number of training posts available under the new system as was available under the old.
"Those doctors unable to secure a training post will be eligible to apply for non-training posts and, if they choose, to compete for a training place again next year", Dr Burns added.
Shona Robison, the SNP's health spokeswoman, who spoke at the rally, agreed with junior doctors that the reforms were not working, telling them: "The fact that you are here is testament to that.
"If we don't do something to avert this, we're very much going to have a crisis on our hands.
"Your future careers and whether or not you stay in Scotland are at stake and that's what I'm worried about.
"My concern is patients will be the ones to suffer because we will lose services, and I don't want that to happen."
The rally also heard from independent MSP Dr Jean Turner, a former GP.
She said: "The Government is doing a grand job of wanting to kill the NHS and shoot us all in the heart."