The most substantial difference between the two bills is the approach to the airport screening process. The Senate bill would federalize the airport screening process, while the House bill would give the President the flexibility of adopting either a federal-private sector coordination or federalizing the airport screening process. The private-federal model requires the federal government to provide an average of 10 to 15 percent of security personnel while the private sector provides the remaining 85-90 percent of security personnel. In a letter to House Speaker Dennis Hastert (R-Ill.) on October 25, 2001, the President expressed his support for H.R. 3150. The President explained H.R. 3150, similar to his proposal, would give the "federal government the flexibility to build the best workforce to perform the actual screening function". The President stated in the letter, "Such an inflexible, one-size-fits-all requirement fails to permit security tailored to the very different circumstances that exist at airports across the country." The House narrowly defeated an amendment proposed by Representative Oberstar (D-Minn.) comprising the Senate-passed language that federalizes the system of passenger inspection. The vote on Representative Oberstar's amendment was 214 to 218. A passenger facility fee of $2.50 charged for each one-way trip would cover the cost of increased security. If the fee imposed on passengers is insufficient to pay for the costs of the increased security, a fee will be imposed on the air carriers for the difference between the security cost and the amount collected from passengers. The legislation also makes flexible funds under the Airport Improvement Program and Passenger Facility Charges if the fee or grant is used to improve security at the airport.

H.R. 3150 would establish a new Transportation Security Administration at the Department of Transportation that would oversee security measures for all modes of transportation. The Transportation Security Administration would be headed by a new Under Secretary of Transportation for Security. The Under Secretary of Transportation would oversee an expanded federal air marshal program. The Under Secretary would be required to develop methods to strengthen cockpit doors, provide for the use of video monitors to alert the cockpit crew to activity in the passenger cabin and for other innovative technologies. The bill authorizes $500 million to air carriers to carry-out increased aircraft security measures.

The manager's amendment would extend $1.5 billion of airport assistance for their increased security expense for FY 2002 and FY 2003. The amendment would strengthen existing language in the bill on the screening of checked baggage and sets a deadline for screening of all baggage for December 31, 2003. The amendment includes a provision that would deputize screeners as federal transportation security agents and would ensure that such agents would operate under universal standards, badges and uniforms. Language in the amendment would cap liability limits of insurance coverage and provide a broad immunity to entities such as Boeing Corp.; Port Authority of New York and New Jersey and the Fire and Police departments of New York City.