The Navy recently restarted the program, inviting the two companies to submit fixed-price proposals for three additional ships. Lockheed, still hoping to win the entire prize, said the problems encountered with the Freedom would not be repeated, now that the company has a finished design.

“It will be great, the next time around,” said Mr. North, the program manager. “Lead ships are truly hard.”

Navy and industry officials say blame for the program’s rocky early history has to be shared.

“It’s easy to lay all the blame at the foot of the government, and the Navy was naïve, but the companies bear some of the responsibility,” said a senior industry official who asked not to be identified because of his involvement in the project. “They were playing the game to get the contract, not owning up about all the issues until well into the game, hoping to make some recovery downstream.”

Mr. McCreary, the Marinette general manager, said that while the shipyard might not have fully mastered the Navy’s accounting system, it had given the Navy frequent progress reports showing problems mounting.

Mr. Winter, the Navy secretary, complained that the Navy bureaucracy had failed to alert him to rising costs. The Pentagon, he said, was bedazzled by the idea of saving money and time with commercial technologies.

“It got oversold,” he said. “The concept was just abused.”

He lamented the Pentagon’s eroding expertise in systems engineering  managing complex new projects to ensure that goals are achievable and affordable  and faulted the notion that industry could best manage ambitious development projects.

“Quite frankly, industry is not good at doing this,” he said.

Recently, Mr. Winter said, he instituted new procedures to ensure tighter supervision of all shipbuilding projects. He says he is confident that the coastal-ships program will produce a fleet of fine, affordable vessels. But as he contemplates the Navy’s long-range rebuilding plans, he says he stands behind a scorching critique that he delivered at a convention in Washington last year:

“If we do not figure out how to establish credibility in our shipbuilding programs and plans, and restore confidence in our ability to deliver on our commitments, we cannot expect Congress or the nation to provide us with the resources we so urgently need.”