But the US tycoon has already declared he will try to fight the firm's appeal.
The substation was planned for the small community of Blackdog but it met with stiff local resistance, with 62 out of 85 residents writing to protest, after a series of surveys uncovered traces of asbestos and other contaminants.
Last October the Formartine area committee of Aberdeenshire Council refused permission for two electricity substation buildings and ancillary works on the former landfill site, and for an underground cable route between the substation and the landfall of the connector to the wind farm. The Scottish Government had approved the £230 million 11-turbine European Offshore Wind Deployment Centre (EOWDC) in March. It would not be a commercial wind farm but a testing centre for offshore developers.
However the Trump Organisation is convinced it will blight its nearby £750 million golf development at Balmedie, north of Aberdeen, and has challenged the Scottish Government's decision at the Court of Session
The project partners behind EOWDC have now lodged an appeal with the Scottish Government. Speaking for the partners Andy Paine, head of offshore wind development for Vattenfall in the UK, said: "The project partners have made every effort to engage and work closely with the local community to assure them that finding low level traces of asbestos in the ground is not unusual for a brownfield site such as this."
He said they were committed to improving the area of ground if consent was granted for the onshore works in order to render it safer and of a higher quality than at present.
As part of the appeal, an independent site-specific asbestos risk assessment of the proposed development had been undertaken to provide further reassurance with about the asbestos risk and how this would be managed during construction, he said.
But George Sorial, executive vice-president and counsel of the Trump Organisation, issued a statement from New York. He said: "We have already instructed our legal team to challenge the appeal and fight every aspect of this terrible scheme.
"The Formartine Area Committee determined that Vattenfall's proposal, which would be constructed over a toxic landfill site, is dangerous and puts many lives at risk. This project is fraught with insurmountable problems and the worst type of politics. It would be a financial and environmental disaster for Scotland."