In a 10-page order on Thursday, US District Judge Richard Leon modified the wording of an injunction he issued on March 31 that had ordered construction to stop, to address Trump and federal agencies' "brazen" and "disingenuous" interpretation of that earlier ruling.
The National Trust for Historic Preservation, a non-profit charged by Congress to help preserve historic buildings, sued the administration, asserting Trump exceeded his authority when he razed the historic White House East Wing last October and began construction of the planned 8360-square-metre ballroom, which is costing more than $US400 million ($A560 million) and being funded by corporate donors.
Leon said he was clarifying the scope of his earlier order to stop "above-ground construction of the planned ballroom" but not "below-ground construction of national security facilities".
The judge's original March 31 order said much of the work needed to stop but that crews could continue "construction necessary to ensure the safety and security of the White House."
Trump and federal agencies then asserted in court filings that the judge's national security exception applied to the entire project because of elements of the ballroom like missile-resistant columns and drone-proof roofing.
The Trump administration also argued that the ballroom and a planned military bunker underneath it are a "single, coherent whole".
Leon wrote in Thursday's order that Trump and federal agencies "now seek to turn this exception on its head and unreasonably insist that the entire ballroom project may proceed".
"I cannot possibly agree," the judge wrote.
In a series of social media posts on Thursday, Trump called Leon a "highly political" and "out of control" judge.
The ruling prevents future presidents from having access to "bomb shelters" and "a State of the Art Hospital and Medical Facilities," Trump said, "which all means that no future President, living in the White House without this Ballroom, can ever be Safe and Secure at Events, Future Inaugurations, or Global Summits."
Former Republican president George W Bush appointed Leon.
The Trump administration said in a court filing it would appeal Thursday's order to the US Court of Appeals for the District of Columbia.
The National Trust for Historic Preservation had asked Leon to clarify his earlier injunction. After Trump appealed, the DC Circuit last week had also instructed Leon to revisit its scope, citing Trump's arguments about national security.
