An appeal protesting the National Oceanic and Atmospheric Administration's decision to move its research fleet from Lake Union to Newport, Ore., was denied Thursday by the federal Government Accountability Office.

An appeal protesting the National Oceanic and Atmospheric Administration’s (NOAA) decision to move its research fleet from Lake Union to Newport, Ore., was denied Thursday by the federal Government Accountability Office (GAO).

The GAO essentially said the appeal — on the grounds that NOAA’s own environmental analysis shows the new location near the mouth of the Yaquina River is in a flood plain — was not filed soon enough.

It’s the latest in a series of blows for the city of Seattle, Washington’s congressional delegation and owners of the Lake Union property where the vessels are now based. They have been applying pressure to persuade the Commerce Department to keep the four ships and an operations center in Seattle after NOAA’s lease expires in June 2011.

The vessels have been based in Seattle for 45 years.

In August, NOAA awarded a new 20-year lease to Newport. Last month, federal lawmakers and the governor urged the agency to reconsider the move, arguing that separating the vessels from NOAA’s Seattle-based scientists would hurt the agency’s mission.

“I have serious doubts about whether the final award decision is truly in the best long-term interest of NOAA, its scientific mission and its employees,” Sen. Maria Cantwell, D-Wash., wrote in a letter to Commerce Secretary Gary Locke.

It’s not clear what options remain for those trying to reverse the decision.

A decision on a separate appeal filed by the Port of Bellingham, which also hoped to land the the new home for NOAA vessels, isn’t expected until early December.

Craig Welch: 206-464-2093 or cwelch@seattletimes.com