MPs have branded the Department of Health's leadership during last year's reforms to junior doctors' careers as "totally inadequate".
The implementation of Modernising Medical Careers (MMC) saw a number of problems for which the then health secretary was forced to apologise.
In a report on the reforms today the health select committee says the Department of Health (DoH) was "inept" and has since failed to resolve all the problems relating to MMC.
The report also says the introduction of new speciality training arrangements in 2007 was disastrous and resulted in an ineffective short-listing process.
It claims the DoH did not take responsibility for problems resulting from MMC and that the government failed to prevent open access to training for doctors from across the globe in both 2007 and 2008.
The committee says this was "inexcusable" and that it has resulted in hundreds of UK graduates being unable to continue their training.
The government's management of migration and doctors' training places is branded by the committee as "poorly planned, badly communicated and inadequately coordinated".
MPs on the health committee also expressed concern that the Home Office told them it had no plans in place if the Law Lords found the Department of Health's guidance on overseas doctors to be unlawful - which they did in April 2008.
Its report concludes that this issue must be resolved as a matter or urgency.
In January the Tooke Review of MMC recommended that a new body be created to oversee medical training.
This proposal has been described as "problematic" by the health committee, which instead advises that the MMC Programme Board should be supported and its independence strengthened.
Other proposals include an improvement in communication between the DoH and junior doctors and for the chief medical officer's role to be more accurately defined.
Committee chairman Kevin Barron said: "The Department of Health, other relevant government departments and the medical profession must get a grip and resolve this mess that has diminished the reputations of all those concerned and resulted in untold amounts of stress on junior doctors across the country and beyond."
The British Medical Association (BMA) described the committee's report as a "damning indictment of the government's failure to listen".
"The medical profession's concerns were repeatedly and arrogantly disregarded, and thousands of junior doctors paid the price," said BMA chairman Dr Hamish Meldrum.
In response to the report, a DoH spokesperson said it understands the problems caused by the reforms and has apologised for them.
"Since then we have created the MMC Programme Board, over half of which are representatives of the medical profession and junior doctors, to advise ministers on junior doctors training and recruitment," the spokesperson added.
"Every single recommendation of that board has been accepted and implemented by ministers. We now need to consider the committee's report and findings carefully before publishing our response."