U.S. District Court Judge Terrence Boyle said in his eight-page order that the Navy failed to show it would be harmed by waiting until the matter was settled in court.
Navy lawyers earlier this week asked Boyle to allow it to spend about $5.2 million on the outlying landing field in Washington County.
A spokesman said the Navy was disappointed with the decision.
"Every day we are delayed from moving forward on this project is detrimental to the readiness of our forces," Commander Kevin Aandahl said in a statement.
The executive director of Audubon North Carolina, one of the environmental groups opposing the landing field, said he believed the opponents would prevail when the case is heard in 2005.
"It is clear that the area near Pocosin Lakes National Wildlife Refuge is uniquely unsuited to a jet landing field," Chris Canfield said in a statement. "The huge flocks of tundra swans and snow geese that are just now arriving there for the winter present a great hazard to pilots. Attempts to control the birds would require the devastation of the refuge, a globally significant natural resource."
The Navy has said the location is the best fit, with the fewest environmental problems, for flights from bases in North Carolina and Virginia by new F/A-18 Super Hornet jets.
Governments of Washington and Beaufort counties, as well as environmental groups, have sued the Navy over the field.
The opponents contend there are better sites in North Carolina with fewer environmental problems and that the current location will displace farmers who depend on the land for their livelihood.
Boyle earlier had entered an order stopping Navy work on the 30,000-acre project, which would have an 8,000-foot runway that would be used by Navy and Marine fighter jets to simulate aircraft carrier landings.
The Navy likes the site because it is located between Naval Air Station Oceana in Virginia and Marine Corps Air Station Cherry Point in North Carolina, where the squadrons would be based.
The proposed site is also about five miles from the Pocosin Lakes National Wildlife Refuge, home to more than 100,000 wintering waterfowl. Environmental experts have said the waterfowl would be a hazard to pilots and expensive fighter jets nearly half the year.
The Navy already has spent about $6 million on planning, land purchases and environmental studies for the estimated $186.5 million project and argued that additional spending would be minor.
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