The Transit Without Visa and International to International transit programmes had allowed foreigners, who would normally need a visa to visit the United States, to connect to another
international flight without the paperwork.
In a statement, the department said recent intelligence indicated that terrorist groups had been planning to use the programmes to enter the United States or US airspace without being first screened.
"The steps announced today, while aggressive, are an appropriate response to the threat," Homeland Security Secretary Tom Ridge said.
“We know they will have an impact on international travellers, but we believe they are necessary in order to protect lives and property."
"The steps announced today, while aggressive, are an appropriate response to the threat" -- Homeland Security Secretary Tom Ridge
The agency issued a warning to airlines and law enforcement personnel late last month about possible airplane hijackings or bombings.
But they expressed particular concern about people connecting from one international flight to another at US airport without a visa.
The State Department and Department of Homeland Security instructed airlines to stop allowing passengers from using the programmes.
But the agencies said they plan on reinstating the programmes when more security measures are put in place.
The agencies said they would reassess the suspensions over the next two months after reviewing public comments and the latest intelligence.
The Transit Without Visa programme, which began in 1952, permitted passengers who need a visa for entering the United States to stop at up to two US airports and change planes for another foreign destination without a visa.
Those travellers do go through normal border inspection and the airlines were responsible for making sure those passengers who take a domestic flight to a second US airport do not enter the country illegally, by holding onto the person's passport and providing an escort to the next flight.
Foreigners who normally need a visa to visit the United States were allowed under the International to International programme to pass through a US airport to another foreign country without getting the documentation.
In that programme, the passenger is barred from connecting through two airports and must remain in the international transit lounge.