Prime Minister David Cameron's staff say he was aware of the Education Secretary's plans to scrap GCSEs before they were leaked, in contradiction to statements made by Nick Clegg.
The Liberal Democrats expressed fury earlier in the week, when it came to light that Tory Education Secretary Michael Gove had drawn up the proposals.
The documents, which emerged in the Daily Mail, suggested replacing GCSEs with O-levels in traditional academic subjects such as English, maths, and science.
The Deputy Prime Minister told reporters: "This has not been subject to collective discussion in government. Neither myself nor the Prime Minister were aware of it. That's self-evidently the case."
He indicated that Mr Gove stood no chance of making his reform plans government policy without the support of his Lib Dem colleagues, simply stating: "If Michael Gove wants to turn some of his ideas into government policy he's entirely entitled to put that forward for wider discussion."
He added: "By definition, in a government, if you have collective agreement, and particularly in a coalition, it requires support from all sides."
However, in a contradiction which is likely to cause more strife between the coalition partners, Number 10 has now indicated that Mr Cameron had discussed the plans with Mr Gove previously but had not expected them to become public.
A senior aide indicated that the PM was in favour of exam reform, but stopped short of endorsing Mr Gove's specific plans.