Waste management group arc21, which represents six councils in Northern Ireland, plans to co-locate a mechanical biological treatment plant and an energy from waste plant at the Hightown Quarry site near Mallusk.
The plans were approved by a senior civil servant at the Department for Infrastructure in September last year, following a recommendation from a Northern Ireland Planning Appeals Commission (PAC) report which noted the strategic need for the facility, its compliance with regional waste policy and the environmental benefits it would deliver.
However, local campaigner Colin Buick earlier this week succeeded in a High Court challenge against the refusal.
In her judgement decision, High Court judge Mrs Justice Keegan said that it is a "common case that the impugned decision was taken in the absence of a minister with responsibility for the department there having been no executive in Northern Ireland since January 2017".
However, the judge said that, despite the absence of a working Northern Ireland Assembly and minister, the decision still should have been made by a minister and not civil servants.
She said that she had "no reason to doubt" that the civil servant "acted in good faith" in approving the application.
But she added, "as he recognises himself, decisions have to be taken in a lawful manner otherwise the whole structure of government is undermined".
The Department for Infrastructure annouced yesterday that it would appeal the decision.
The department said that it was "seeking clarity on the law in this case and in relation to decision making on other regionally significant planning applications."
It said: "The department is clear that it would be preferable for these decisions to be taken by ministers, however it has a duty to process planning applications and other planning cases and failure to do so has wide ranging implications for the Northern Ireland economy and the environment. It is therefore important to have clarity on the legal position in the continued absence of ministers.
"While the appeal process is underway, the department will not take any further decisions on regionally significant applications and continues to carefully consider the full implications of the judgment on other planning cases. The department will continue to progress applications in readiness to reach a final decision."
The Becon Consortium, which is delivering the project on behalf of arc21, said: "We note that the decision not to uphold this decision does not change the material facts at the heart of the planning decision, the project’s compliance with regional waste policy or indeed remove the strategic need for such infrastructure here in Northern Ireland in the future.
"Instead, the judge’s decision is entirely based on procedural matters in relation to the ability of the department to make a decision in the absence of a minister in post.
"While this a frustrating setback, we remain fully committed to delivering this project on behalf of arc21 and will now take time to consult with them, to consider the implications of this decision and agree the next steps to move this strategically important infrastructure project forward."