The GAO said in a September report to Congress that the installations were redundant and incompatible and failed to meet Navy requirements because of their limited scope. "In short, the efforts were failures, and $1 billion was largely wasted," the GAO said.

The latest project, an $800 million ERP project that was begun in 2003 and slated to go live in 2011, is also in jeopardy, the GAO said -- unless best practices are adopted and followed.

The Navy vigorously disagreed with the charges and recorded its dissent with the GAO. "Both the [Department of Defense] and the Department of the Navy are quite happy with how the pilots have gone," said Tim Hollande, deputy director of Navy ERP programming. "We've gotten a tremendous amount of knowledge in how to do an enterprise solution in a military environment."

Prior to the pilot projects, Navy officials were uncertain whether such implementations were feasible, he said. Now, the Navy is comfortable it can do them. "We think we got a lot of value," said Hollande.

He said there was minimal overlap among the various applications' functions and added that the pilot projects allowed the Navy to take 89 legacy systems off-line.