The Strategic Development Plan 2 (SDP2) sets out the vision for the long term development of the south east of Scotland, including the Edinburgh city region.
The draft plan has been prepared by the South East Scotland Strategic Development Planning Authority, (SESplan), a partnership of six member authorities including Edinburgh, East Lothian, Midlothian, Fife, Scottish Borders and West Lothian.
The first SDP for 2009 to 2032 was approved by Scottish ministers in June 2013. The second version, covering the period 2018-2030, was submitted for examination in 2017.
The plan sets a housing target of 63,852 homes over the plan period, averaging at 5,321 homes per annum.
Following its examination, ministers have now written to the authority informing it that they have decided to "reject" the plan.
The letter says the key grounds for this decision were that they were not satisfied that the plan "has been informed by an adequate and timely transport appraisal".
The note said concerns about the adequacy of the approach taken to the transport appraisal "were repeatedly raised by the Scottish Government throughout the preparation of SESplan 2. These concerns have not been adequately addressed by the authority."
Ministers went on to say that the plan "does not take sufficient account of the relationship between land use and transport".
It also "does not properly acknowledge and address the region’s infrastructure constraints to support the spatial strategy for delivering housing land across the area," they add.
"Ministers do not consider that it is acceptable to approve the plan as to do so would be to adopt a spatial strategy which is not supported by an adequate assessment of the transport impacts or by an adequate strategy to mitigate its impact on the strategic transport network," the letter said.
The letter added that ministers "do not support the use of supplementary guidance to resolve this issue".
It says that Scottish Planning Policy states that any transport appraisal should be carried out "in time to inform the spatial strategy of the plan".
"Adoption of the plan, ahead of the preparation of supplementary guidance on transport, is not considered by Scottish Ministers to be an acceptable solution," it says.
SESPlan said it was "very disappointed" at the decision, adding: "SESplan authorities will now consider the details of the minister’s letter."
The new Scottish Planning Bill proposes abolishing the country's four city region strategic development plans. Instead, it envisages that the National Planning Framework, Scotland’s overarching spatial plan, would set out regional planning priorities.