The job losses, which represent a quarter of the workforce, come at a time when the DfE is creating more academies and free schools as part of its drive to move away from local authority control of schools and give schools greater autonomy.
The move shows that Mr Gove is prepared to go further than other government departments in making savings, which will increase the pressure on his Cabinet colleagues to follow suit.
The announcement comes after an MPs’ report revealed low morale within the department and found that constant changes at the DfE were shifting policy away from children’s issues and towards the management of schools.
However, an internal review into how the DfE works found that decision-making was often “slow and laborious” with “unclear roles and processes”. The allocation of work needed to be more aligned with the strengths and skills of the staff, it said.
The move to close six regional offices and streamline the department, saving £290 million by 2015/16, has worried unions and the opposition.
Stephen Twigg, shadow education secretary, said: “While Labour supports efficiency savings in the civil service, this review says certain work that isn’t a ministerial priority will stop, raising the prospect that programmes and services will be axed. Michael Gove needs to explain to parents how this will affect them.
“Two weeks ago the Education Select Committee warned that children’s policy was in danger of withering. Now these leaked plans makes no mention of children’s policies – services like Sure Start and support for vulnerable children or those in care. It focuses exclusively on academies and free schools. Policies must be based on what families want, not out of touch ministers.”
A spokesman for the Public and Commercial Services Union said Michael Gove was trying to run the DfE “as some kind of nightmarish, right-wing experiment, playing politics with people’s livelihoods and putting at risk the important services these civil servants provide to teachers and the public”.