"We need to find out why, and how it can be brought back to have a registry that has credibility," said North Dakota Sen. Byron Dorgan, a Democrat.
The FAA says as many as 119,000 of the 357,000 U.S.-registered aircraft have "questionable registration" due to missing paperwork, invalid addresses and other paperwork problems.
In reports in 2007 and 2008, the agency warned that the probblem was causing loopholes that terrorists, drug traffickers and other criminals might exploit. It was concerned that a criminal might use a U.S. registration, known as an N-number, to slip by computer systems designed to track suspicious flights.
"It is advantageous to a drug trafficker or a terrorist to use an airplane with a registered N-number as these airplanes would be subject to less scrutiny," the FAA wrote in a 2008 explanation of the registry problem.
On Friday the FAA said it was taking "proactive steps" to clean up the database by requiring all aircraft owners to re-register their planes over the next three years.
All plane owners are required to re-register their aircraft now that it's known the FAA's records are in disarray.
For most owners -- like A and M Aviation president James Harvilchuck who has eight planes based at Bolingbrook's Clow International Airport -- it's not a problem.
"As plane owners, we're not that concerned about it. It's easy to do," said Harvilchuck.
And most pilots are well aware at Clow that registration information is posted and it can be done online.
"It was a click and enter and I'm done. Basically, that was it. Just sent it back. It was that simple. But I'm a good guy. I don't know what the bad guys are doing," said Joe DePaulo, Clow airport manager and plane owner.
And therein is the issue. Earlier this year, the country witnessed the danger when a man upset with the government crashed his plane into the IRS building.
The fear is that a drug dealer or terrorist might buy a plane and the government would never know because of shoddy records.
"Someone could be flying a plane into a nuclear plant or a chemical plant or an iconic building. I think this is an area where it's time that the FAA got down to business of knowing who owns the aircraft," said Richard Ben-Veniste, ember, 9/11 Commission.
All US registration numbers start with N and must be on the tail or fuselage. The numbers are used for flight plans and by air traffic controllers.
In the end, plane owners who refuse or fail to re-register will lose their certificates and, with that, flying privileges. The planes will then be grounded.
The Associated Press contributed to this report.