Education Secretary David Blunkett has asked Halton in Greater Manchester, Liverpool, Rotherham and the London boroughs of Hackney, Islington and Southwark to rethink their plans.
In three cases - Hackney, Halton and Liverpool - the Department for Education and Employment said there was need for a major overhaul.
For the other three, it said the combination of serious concerns and a recent or imminent Office for Standards in Education inspection made it right to call for an early review.
Education development plans - a requirement of the School Standards and Framework Act - have a three-year lifespan. They focus on a council's strategy for raising standards and include targets agreed with schools.
Mr Blunkett has given the plans prepared by the six councils approval for just one year and said: "We believe EDPs should be challenging and robust in order to deliver clear objectives.
"There are almost 100 LEAs whose plans are very good indeed. There are some LEAs whose plans need further work and we have asked them to do that."
A number of other authorities will need to revise plans before the second year of their EDP.
Halton said its enthusiasm as a new LEA had probably led to its EDP being too expansive and not focusing enough on key targets. Nevertheless it was surprised to learn it needed a major overhaul.
Hackney is looking at the areas of the plan which the DFEE has drawn to its attention. A spokeswoman said: "We are happy to work with the DFEE to ensure that Hackney is fully developing its education services."
Southwark said it had only produced an interim plan, pending a radical review of secondary education in the borough.
Islington, which is also revamping education, said it had always anticipated resubmitting its plan.
Of the six issues in Liverpool raised in a letter from the DFEE, two were flagged up in the EDP and one - its literacy strategy - had not only been approved but praised by the national director of the literacy programme.
Frank Cogley, Liverpool's education director, said: "We clearly need to explore these issues as there may be some confusion over the messages we are receiving."
Rotherham has been asked to look again at four areas - literacy targets, policies for supporting schools causing concern, success criteria throughout the improvement programme and the delegation of more advisory services.
Tom McCormack, its head of curriculum services and education standards, was disappointed but said it was understandable given the OFSTED inspection of the council this autumn.