The government's curriculum regulator is on "red alert" over its impending move from London to Coventry, which is to happen just as the organisation splits in two.
The changes coincide with the busiest phase of curriculum and exams change in the Qualifications and Curriculum Authority's (QCA) 11-year history.
Changes include the introduction of diplomas, which were themselves hit by controversy last week, when the head of a major exam board said they risked failure.
The dangers to the organisation are highlighted in the minutes of a recent board meeting.
The authority's role of regulating qualifications and monitoring exam boards has been handed to Ofqual, a new organisation, which opened this month in Coventry.
Next year, the remainder of the QCA will complete its move from Mayfair, west London, to the west Midlands city, as part of a Treasury cost-cutting drive.
The Public and Commercial Services union, which represents most of the authority's staff, said it expected 85 per cent of its employees to resign because they are unwilling to leave London.
The union has said this is likely to undermine the authority's ability to monitor the impact of major changes in schools, including the introduction of a new key stage 3 curriculum and the revamping of GCSEs and A-levels.
The board minutes said: "The board decided to change risk 4 - being unable to deliver (its) key remit due to the loss of key staff because of the relocation of the authority - from amber-red to red.
"The board felt that the likelihood of the risk had been increased by the workload and additional staffing requirements due to the split of regulatory functions from QCA."
Last week, Jerry Jarvis, managing director of Edexcel, angered ministers after giving a newspaper interview in which he said the new diplomas were "a huge educational risk".
The board was then forced to issue two statements on its website, saying it remained committed to the courses, which are being phased in from September.
Opinion is split over the diploma's prospects. David Turrell, head of Sir Bernard Lovell School near Bath, which has been piloting a diploma-style system for years, said it had proved a great success.
Jan Panell, a consultant who is working with London local authorities on introducing the diplomas, said: "It's the time frame that's the problem rather than the concept of the diplomas, which offer a genuine alternative to GCSEs and A-levels."