The chairman of the British Medical Association (BMA) wants a "cast-iron guarantee" that no junior doctor will lose out from changes to training.
The row sparked protests by junior doctors around the country
James Johnson told the BMA's Junior Members' Forum the careers of thousands of them could be ruined by the changes.
His call follows criticism of the government's new application process.
Junior doctors said the best candidates for specialist training posts were not being selected, and many were not even getting interviews.
They had complained that the online Medical Training Application Service (MTAS) was causing computers to crash, that non-medics were involved in short listing and there was no facility on the form to attach CVs.
Speaking in Dundee, Mr Johnson said: "It's disgraceful that thousands of our best doctors could have their NHS careers wrecked through no reason other than government mistakes and poor workforce planning."
An earlier review of the MTAS said doctors in England should be guaranteed at least one interview for a traineeship.
But Mr Johnson said whatever happened a "significant cohort" of junior doctors would lose out on training posts
"We will push the government to give a cast-iron guarantee that they will not be forced out of training," he said.
He added that junior doctors should be able to continue in their old senior house officer posts until they can go on to more specialist training and called for a review of the whole Modernising Medical Careers (MMC) programme reforms, of which MTAS is a part.
BMA figures show 34,520 junior doctors are applying for 18,500 specialist training posts.
Last month, junior doctors held protests in Glasgow and London against the reforms.