"This is really a very serious position for all the TEIs," Iain Smith, dean of education at Strathclyde University, said. It faces a pound;1 million loss of income.
The Executive wrote to the Scottish Higher Education Funding Council on March 7 effectively overturning guidance issued only the previous month which forecast similar intakes to this session. The institutions then made legally binding offers of places.
There will now be 2,291 funded places on initial teacher education, 327 fewer than this year. This session TEIs were funded to take an additional 422 students as a result of the post-McCrone settlement.
The problem has arisen over continuing difficulties in implementing the deal, particularly in finding posts for graduates guaranteed a training year.
A spokeswoman for the Executive said: "The revised guidance reflects the information we have received from local authorities which suggests that it will be a challenge for them to provide the number of training posts required to place all eligible students this year (approximately 2,400). In the circumstances, the only sensible course of action was for us to revise the intake figures accordingly."
Institutions are obliged, under the clearing arrangements, to make offers during February and March for those who have applied by the December 15 deadline.
"What really annoys us is that there is this complete assumption that the TEIs can turn taps on and turn taps off when dealing with the intakes of students," Mr Smith said. "No organisation or business can operate on that basis."
Universities had invested heavily in staff and facilities to plan for the extra teachers the Executive said would be required over the next six years. They now face having to review their plans.
The Executive spokeswoman said: "If individual TEIs have specific concerns about the revised guidance we are, of course, prepared to discuss these issues."