Five years, millions of dollars and innumerable headaches later, the Transportation Security Administration (TSA) still has not put in place the sophisticated terrorist screening facilities it promised to install at the nation's airports and ports after the Sept. 11, 2001, terror attacks.

TSA officials have confirmed to FOXNews.com that Secure Flight, the terrorist screening program that would check passengers against a massive federal terror watch list, won't be up and running until the database is complete, and no deadline has been set for completion.

But while Congress is both surprised and concerned at the apparent lack of progress, TSA officials say reports that the pilot program has been sent "back to the drawing board" are misleading.

"Our focus is on getting it right, not setting specific timetables," said TSA spokeswoman Ellen Howe. "There have been some challenges, but we're getting it right, and the process is moving forward."

Secure Flight, which has had previous incarnations in the aborted CAPPS I and CAPPS II screening projects, has been hindered by problems such as whether TSA can protect passengers' privacy. According to Howe, the agency has already spent $135 million on building Secure Flight, and $35 million more has been dedicated to it but not spent yet.

In February, TSA suspended Secure Flight for a "comprehensive audit" after the U.S. Government Accountability Office (GAO), Congress' investigative arm, said the program was still lacking fully defined requirements and policies dictating what personal information would be used for traveler screening. The agency had also not demonstrated how it would protect privacy. Howe said the agency did a "baseline" restructuring of the program to meet the GAO's concerns.

In the meantime, TSA officials have put the onus largely on the private sector to get the awaited Registered Traveler program moving forward. This program, which has been tested through private vendors at select airports, would allow frequent travelers who have already passed background checks through airport security faster.

But Registered Traveler -- at a cost so far of $25 million, mostly for the pilot program -- has stalled, say officials, while the vendors hammer out critical details of the program.

Finally, the Transportation Worker Identification Credential program, which would require background checks and special IDs for 750,000 port employees in the country, has been hindered by technical obstacles, cost overruns and insufficient testing, according to a GAO report released in October.

TWIC, which has already cost $81 million, according to officials, is still in the bidding phase for contractors and is far from ready.

Members of Congress who oversee TSA, a component of the Department of Homeland Security, expressed frustration with the lagging credentialing program.

"We have lost precious time that we can ill afford to waste," Sen. Joseph Lieberman, D-Conn., said in October. He will become chairman of the Senate Homeland Security and Governmental Affairs Committee in January. "TSA dropped the ball on the TWIC program, and as a result, millions of taxpayer dollars had been wasted and an effective ID program for port and transportation workers in not yet in place."

Howe said adapting to and incorporating new and evolving technology has been a challenge. For example, the GAO noted in its October report that it was still unclear whether the TSA had found the right biometric technology to prevent security breaches in the worker credentialing program.

"We're trying hard, and it's taken some time, but we are on track," Howe said.

Fundamentally Flawed or Bureaucratic Blunders?

Critics say that considering the stakes -- the primary one being preventing another terrorist attack in the United States -- time is of the essence.

"It's just more bureaucratic nonsense," said Erick Stakelbeck, a Washington-based counterterrorism analyst. "Five years after 9/11, not to have these programs in place is just a disgrace."

Brian Riedl, lead budget expert at the Heritage Foundation, said stories abound in every federal agency about multimillion dollar programs and their failures to deliver.

"In general, it's not a surprise to see very expensive programs fail to exhibit positive results," he said. "In fact, the government's own auditors cannot find evidence of achievement in 38 percent of all federal programs."

He added that if programs aren't even launching, "then that is a very disturbing sign."

Riedl said that aside from the usual bureaucratic inefficiencies, members of Congress like to meddle with legislation and contracts, making it more difficult for new programs to get off the ground.

"You're dealing with hundreds of millions of dollars and a huge bureaucracy -- in this case, a new agency. That would be a challenge for any agency," he said.

Chuck Pena, defense expert for the Independent Institute in Washington, said the difficulties may also lie in trying to implement a program like Secure Flight because it relies so much on effective and accurate cross-checking of private and public data.

Right now, airlines check passengers' names against terror watch lists provided by the government. The government will take over that function when Secure Flight is running. The GAO reported in September that misidentifications continue to hamper the effectiveness of terror screening.

"It's not just the false positive, getting the wrong guy. But it's the cost. It takes up resources," said Pena. "If you have too many false positives, you're wasting money, and time. That's the big problem."

James Harper, privacy expert for the libertarian-minded Cato Institute and author of "Identity Crisis: How Identification Is Overused and Misunderstood," said the programs are flawed because bad people will always find a way around security measures built on identification.

"[Identification] is a weak and expensive method," he said, noting that the TSA should put its resources into screening for explosives and other detection technology at airports and ports.

Nevertheless, the airline industry is hoping that some sort of workable, uniform program, particularly for screening passengers and workers, will be rolled out soon.

"We think they are great programs," said John Meenan, executive vice president of the Air Transport Association, which represents nearly all of the domestic airlines in U.S.

"I think it's fair to say we are all interested in seeing seamless, efficient programs developed that advance security," he added. "At the same time, there are very complicated issues involved and we are trying to work with the appropriate agencies involved and I'm sure there is a frustration in the government with trying to get these programs rolled out."

Sen. Susan Collins, R-Maine, outgoing chairwoman of the Senate Homeland Security and Governmental Affairs Committee, said Congress plans to continue to work on the TSA's shortcomings in the next session.

"Our committee will continue to keep a watchful eye over our nation's transportation system and help close serious security gaps," she said in a written statement.