Proposals to develop the facility at Kingsford were put on hold in October to give planners more time to discuss the plans.
In January, Aberdeen City Council overwhelmingly approved the after accepting a recommendation from planners to give the scheme the go-ahead.
The Scottish Government has now told the local authority that it will not call in the planning decision, leaving it instead for the council to determine the application.
An Aberdeen City Council spokesperson said: "The Scottish Government has written to Aberdeen City Council 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.
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"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."
Aberdeen FC 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."
However, community campaign group No Kingsford Stadium said the Government's decision "now leaves the way clear for the decision to be examined through the courts".
The organisation has so far raised over £40,000 towards a funding target of £60,000 to mount a legal challenge.
"We believe that the decision by Aberdeen City Council is unlawful and we will seek to prove that the council has failed to legally process and consider this application," the group said.
(LM)
