Both of those big-city airports routinely suffer security line delays. The Federal Aviation Administration reported Monday there were no significant flight delays in either Los Angeles or Chicago.

Napolitano, who spoke at a Politico-sponsored event on the 10th anniversary of DHS, said delays will become worse. The Transportation Security Administration and Customs and Border Protection agencies, which are part of the Homeland Security Department, are in the process of issuing furlough notices and have cut overtime for employees.

CBP said in a statement later Monday that weekend delays in Los Angeles and Chicago were caused by "reduced primary booth staffing" because of cuts to overtime. CBP said wait times for passengers on 56 arriving flights at John F. Kennedy International in New York exceeded two hours, and passengers on 14 flights waited more than three hours. Delays at Miami International Airport of more than two hours were reported for 51 flights, and passengers from four flights experienced waits of about three hours. CBP said such waits were longer than usual.

TSA, which is responsible for screening passengers entering airports, said travelers can expect longer security checkpoint lines as the agency reduces overtimes and freezes hiring. TSA said in a statement that it expects to have about 1,000 vacancies by Memorial Day and as many as 2,600 by the end of the budget year in September.