The decision paves the way for the football club to replace its current home of Pittodrie with a £50 million stadium and training complex the other side of the city at Westhill.
However the stadium plan has divided opinion in Aberdeen, with slightly over half of residents in favour of the relocation.
Aberdeenshire Council had also objected to the plans on parking grounds among others and, in doing so, ensured formal notification had to be given to Scottish ministers, who then had the opportunity to call in the application for determination.
But today the Scottish Government has told Aberdeen City Council that planning decision should rest with the local authority.
An Aberdeen City Council spokesperson said: “The Scottish Government has written to Aberdeen City Council today to say it is not going to call in the Kingsford Stadium planning decision, leaving it for the council to determine the planning application.
“The Scottish Government said in the notification that the issues raised by Aberdeenshire Council ‘are not of national significance to have bearing’ on the decision not to call it in.
“The notification further said the Scottish Government expects Aberdeen City Council to have regard to the matters raised by Aberdeenshire Council. We will accordingly consider these matters and liaise with colleagues at Aberdeenshire Council on these matters as necessary.”
Reacting to the news, AFC chairman Stewart Milne said: “We welcome the Scottish Government’s confirmation that Aberdeen City Council can proceed to determine our planning application. We are keen to begin construction of the community and training facilities as soon as possible.
“The next step is to progress the terms of the legal agreement with Aberdeen City Council and work with all stakeholders on agreeing and meeting the conditions.
“We will continue to work with the City, Aberdeenshire Council and the community in the lead up to and during construction. Together, we can deliver a first-class facility to be proud of that will unlock the potential of the Club, the Trust and the next generation of football stars, while making a positive contribution to the local economy.”