Up to 200 trainee doctors hoping to plug Australia’s yawning doctor shortage could have their careers terminated by a bungle that has denied them ongoing positions in Victorian hospitals.

Late on Monday, hundreds of first-year interns discovered that a controversial computer matching system had knocked back their applications for a permanent gig, effectively leaving them out of a job. This morning, rumours were sweeping the state’s hospital wards that the mismatch between applicants and positions was at least 160, and could top 200.

Crikey understands that hospital HR managers met with the Postgraduate Medical Council of Victoria (PMCV) yesterday and were told that “there were enough places for interns”, but that many of the available positions were snaffled by more senior pre-vocational doctors — some of whom are international graduates who now want to enter a training program.

Many of those that missed out are Australian citizens. Second year studies are vital for consolidating knowledge but having a forced year off would massively disrupt the learning process.

The controversy comes just two weeks after a storm erupted over the fate of 180 international medical students who were denied Australian internships despite stumping up hundreds of thousands of dollars for their course. Following interstate ministerial crisis talks, an extra $10 million in Commonwealth money was provided to fund 100 places in private hospitals.

Three thousand medical students are set to graduate at the end of this year.

Carol Jordan, the CEO of PMCV, confirmed this year’s shortfall and told Crikey she was currently preparing a brief to deliver to the Victorian Department of Health on the matter that would detail the precise gulf.

While reluctant to be drawn on the specific number on those who missed out, Jordan said that it was possible some might be able to secure a position after the dust had settled in coming months when rejections were factored in. It is not known how this year’s mismatch compares to previous years. One explanation could be a surge in applications for more popular Melbourne positions as opposed to regional gigs.

Under Australia’s expanded medical training program, university graduates are required to complete an intern year to become fully qualified. At the end of that year they are enter a computer matching process to apply for ongoing employment. But at this point, a bottleneck emerges when the system’s lack of training infrastructure becomes clear.

In Australia, it takes about 12 years to become a fully qualified GP. The Commonwealth is currently undertaking a review of medical workforce programs — and employment logjams are one of the main issues set to be raised by the AMA during the consultation process.

In January, the chair of the Australian Medical Association’s NSW Doctors in Training committee highlighted the crisis inside that state’s  hospitals, detailing the log jam that has developed as the flow of junior doctors clog up a stagnant jobs pool unable to cope with demand.

The issue has been decades in the making — the number of medical graduate programs were slashed in the mid-1990s, causing a workforce crisis. The decision was reversed in the dying days of the Howard government when new medical schools were set up and funding bolstered. But crucially, a concomitant investment in downstream training infrastructure was never pursued and now, five years later, thousands of new graduates are scratching around for work as they emerge from undergraduate and postgraduate study.

The Health Workforce 2025 study released by Health Workforce Australia in March estimated that “demand for advanced training places will exceed their availability by almost 1300 in 2025”.

“Although there is a significant increase in both basic and advanced specialist training positions over the projection period, there is an emerging shortage of advanced training positions over the next few years compared with the number of pre-vocational doctors trying to secure a position,” the report said.

This comes despite projections that Australia would need a further 37,000 doctors by 2025 — 25% higher than population growth. Even with the current numbers of doctors being trained, and a record level of overseas-trained doctors, there would still be a total gap of 2700.

The Australian Medical Association said it was investigating the Victorian shortfall this morning and was hoping to put an exact number on it in coming days.