Campaigners want the computerised junior doctors application system scrapped, the High Court has heard.
MTAS has been widely criticised by doctors
A judicial review was told that the new Medical Training Application Services (MTAS) was so unfair that it amounted to an "abuse of power".
Junior doctor pressure group Remedy wants medics to be consulted over what should replace it, the review into the handling of the system was told.
It comes after MTAS has been dogged by controversy in recent months.
The system was introduced as part of the Modernising Medical Careers initiative aimed at cutting the number of years of training needed for doctors to reach consultant level.
It was designed to speed up the selection process, but doctors said the forms were badly worded, did not ask pertinent questions or allow them to set out relevant qualifications and experience, and had no facility for attaching a CV.
This resulted in many doctors not being selected for their first-choice hospital, and a significant number not getting any interviews at all.
Junior doctors applying to start their specialist training this year are having to compete with those who are part way through their training under the old system for a limited number of training posts.
It means over 30,000 doctors are chasing 23,000 jobs.
Following a review, the government guaranteed every applicant an interview for their first preference post.
And ministers have also announced that after the first recruitment round, MTAS will not be used again this year, leaving follow-up recruitment rounds probably involving about 7,000 posts dependent on more traditional CVs.
However, Remedy UK argues the whole process - including the first round of recruitment should be scrapped.
The group has argued that there was no way to compare interviews that took place now, with those that were held during the first round in February.
Thomas de la Mare, representing Remedy in the High Court, said key decisions with a direct and serious impact on doctors were being made "without any form of notice or consultation".
In a court packed with junior doctors and their supporters, he said MTAS was now "so conspicously unfair as to amount to an abuse of power".
And he said it was mystifying why the British Medical Association, the doctors' trade union body, was not supporting its call.
The BMA has argued scrapping the system at this stage would just "prolong the agony".
The hearing continues.