A political row broke out over the 15-page document which revealed the Scottish Parliament's legislative programme for the next four years.
The document outlined 27 new pieces of legislation, including reform of divorce and adoption law and a shake-up of the Scottish courts system.
However, the Executive moved quickly to insist that one of the most controversial elements of the programme - a proposal to remove schools from council control - had been 'overtaken by events'.
'The debate on school education, which took place in Scotland from March to the end of June, has meant things have moved on and the plans to 'break the local authority monopoly' have been overtaken by events.'
He said he believed the paper in question was a draft which had not been considered by ministers and did not mean the future programme was 'cut and dried'.
'It is sensible to plan, particularly for the first year of next Parliament,' he said.
But opposition politicians seized on the confidential document as evidence that Labour and the Liberal Democrats have thrashed out a back-door coalition deal before the electorate has the chance to cast their votes in May.
A spokesman for the Convention of Scottish Local Authorities said: 'Local authorities are the custodians of the education service in Scotland and we have assurances from the first minister and the education minister that this will remain the case.
'I also understand no case was made during the recent education debate to change the status quo.'
The Executive's preliminary response to the debate will be published in the new year.