Mark Pattison was appointed chief executive of the national strategies in March last year when the private company Capita won the five-year contract.
Mr Pattison had been briefing officials at the Department for Education and Skills twice a week, but the relationship is thought to have become fraught.
When Capita took over, the Government beefed up the strategies so that they became the major mechanism for ministers to achieve targets for test and exam results. One source said the DfES was portraying Mr Pattison as the sacrificial lamb required by the Government to atone for disappointing key stage 2 results.
The Government came under fire this year for "burying" the key stage 2 results by publishing them at the same time as the more positive GCSE results. They showed primary schools had missed the Government's target in national English and maths tests.
On Tuesday, Ian Harrison, Capita's managing director of the strategies, wrote to several education agencies saying he was taking over on an interim basis as Mr Pattison moved on to "new challenges". He wrote: "The DfES has indicated that it is keen to take a more direct role in the strategic leadership of the national strategies with Capita."
A Capita spokeswoman said the DfES played no role in Mr Pattison's departure.
Mr Pattison came to the role with impeccable New Labour credentials. He had been at Bradford council where he turned around the authority's failing privatised education services. Before that he had been director of education at Blackburn with Darwen council, where he also worked closely with private contractors.