Hospitals are facing problems as 30,000 junior doctors start jobs in England, the British Medical Association says.
MTAS was introduced to recruit trainee consultants
According to the BMA, operations and clinics will have to be postponed as NHS trusts rush to fill vacant posts "up to the eleventh hour".
There are twice the normal number of junior doctors beginning jobs on Wednesday because of a shake-up which has ended staggered start days.
The government says NHS trusts have plans to ensure services run properly.
The changes to start days, under the Modernising Medical Careers programme, is designed to speed up the time it takes to become a consultant.
It follows reforms in junior doctor training and the introduction of the controversial online Medical Training Application Service (MTAS), which has proved unpopular with junior doctors.
JUNIOR DOCTORS FIGURES
30,000 junior doctors start jobs on 1 August
Of these just over 14,000 have been appointed through MTAS
13,000 junior doctors are still looking for posts, but fewer than 4,000 of these are UK graduates
On top of the 1,000 MTAS posts still to be filled, the government plans to create up to 1,000 new posts to bail out unsuccessful first-rate candidates
Junior doctors who fail to get a training post can bid for one of up to 8,000 lower status NHS service jobs
Medics have complained that application forms were badly worded and resulted in many of the best candidates not getting jobs.
A group of doctors called Remedy UK even took legal action seeking to overturn the whole process.
A judge ruled the interviews which had taken place should stand, but the government did decide not to use MTAS in the second recruitment round which is running until the end of October.
Critics had predicted thousands of training posts would remain unfilled, but on the eve of Wednesday's start day, over 90% of the 15,600 posts had been filled.
However, there has been a last-minute rush to fill posts, created by the confusion and controversy surrounding the whole process.
Over 1,000 appointments were made in the last three weeks of July alone.
The remainder of the 30,000 new appointments starting on Wednesday are positions recruited outside the MTAS process.
The BMA said the frantic nature of the recruitment process was causing problems.
It said consultants were unable to plan operating lists because they did not know which junior doctors would be on their team.
They also said junior doctors were missing work because of last-minute interviews.
Dr Ian Wilson, deputy chairman of the BMA's consultants committee, said: "Posts have been left unfilled up to the eleventh hour.
"Any forward planning has been impossible. It's inevitable that more operations and clinics will have to be postponed."
Dr Tom Dolphin, of the BMA's junior doctors committee, added: "There has been appalling confusion in the NHS over the last few weeks."
Dr Matt Jameson Evans, a spokesman for Remedy UK, said: "There is likely to be widespread problems, particularly in trusts where the fill-rate is low.
"The whole process has been a disaster from start to finish."
However, the government remains confident any disruption will be kept to a minimum.
Deputy Chief Medical Officer Professor Martin Marshall said: "We know that August is always a quiet month with fewer outpatient appointments and fewer operations, which is why the junior doctor rotation happens at this time every year.
"The numbers involved will be higher this time, but NHS trusts are used to dealing with this issue and have plans in place to make sure services run properly during August."