The system of planning teacher training in England has broken down and risks a future shortage of teachers, a university think tank says.
The Department for Education has switched about 9,000 teacher training places from universities to schools under its School Direct programme.
But Million+ predicts, with only 45% of places on it filled, there will be 3,000 fewer teachers trained by 2014.
The government said heads were choosing "only the brightest graduates".
A spokeswoman for the Department for Education said the programme was "a response to what schools told us they wanted, a greater role in selecting and recruiting trainees with potential to be outstanding teachers".
The spokeswoman said the programme was proving "extremely popular". By May some 22,500 people had applied for half as many places.
She added head teachers had rightly been choosey, only accepting graduates with the highest skills.
The Commons Education Select Committee is conducting an inquiry into teacher training and has just published evidence submitted to it.
In her evidence to the committee, Pam Tatlow, chief executive of Million+ - a think tank that also represents newer universities - said School Direct, , which is focused around on-the-job, school-based training, had been introduced "without any robust assessment of its impact on teacher supply".
"Ministers say that schools should lead the commissioning of teacher training, but it is clear that this will not guarantee the number of trained teachers that will be needed by schools across the country in the future.
"Universities that have run very successful programmes to enhance the expertise of prospective teachers in key specialist shortage subjects are not being allocated numbers."
She added: "The combined impact of the new Ofsted regime under which fewer schools are being classed as outstanding, new rules which debar universities rated as good teacher training providers from having any guarantee of training numbers and the transfer of places to schools which are clearly finding it difficult to recruit suitable applicants has created a triple whammy.
"As a result the national system for planning and delivering an adequate number of qualified and trained teachers has broken down."
Ms Tatlow added: "Universities which have been at the heart of high quality teacher training are being side-lined and expected to take all the risks with no guarantee of training numbers. This is clearly untenable.
"MPs should be very concerned that well-regarded higher education providers will pull the plug on teacher training altogether because of the uncertainty that has been created."
She said: "Rather than expand the programme, School Direct numbers should be reduced in 2014-15 and a national strategy agreed to bring some stability and common-sense back into the system."
Kevin Brennan, Labour's shadow school's minister, said the government's "failure and incompetence means there is now a crisis in teacher recruitment".
"We have already seen 6,000 teachers quit the profession on [Prime Minister David Cameron's] watch, now it looks like there will be a shortfall of 3,000 teacher trainees on top of that.
"This is a real risk to standards, and parents will be worried.
"David Cameron is damaging standards by allowing unqualified teachers into our classrooms.
"This is not the answer to the recruitment crisis he has created. Pupils deserve better."
The Million + study comes after analysis by leading teacher recruitment expert Prof John Howson, of Oxford Brookes University, revealed that by early July schools had accepted only 5,000 trainees on the scheme.