The stricter security measures follow what authorities say was a failed attempt by a Nigerian man to blow up a passenger jet flying from Amsterdam to Detroit on December 25.
Umar Farouk Abdulmutallab, now in US custody, had been in a database with about 550,000 other suspects since late November, but officials said the government did not have enough information to put him on a no-fly list.
The US currently lists Cuba, Iran, Sudan and Syria as "state sponsors of terrorism" but the air travel directive also includes Afghanistan, Algeria, Iraq, Lebanon, Libya, Nigeria, Pakistan, Saudi Arabia, Somalia and Yemen.
With 13 of the 14 nations cited by the TSA being majority Muslim states, the Washington-based Council on American-Islamic Relations (CAIR), a Muslim civil rights and advocacy organisation, said the procedures amounted to ethnic profiling.
"Under these new guidelines, almost every American Muslim who travels to see family or friends or goes on pilgrimage to Mecca will automatically be singled out for special security checks - that's profiling," Nihad Awad, CAIR's national executive director, said in a statement.
"While singling out travellers based on religion and national origin may make some people feel safer, it only serves to alienate and stigmatise Muslims and does nothing to improve airline security," Awad added.
Nigeria also criticised the measures as discriminatory.
Dora Akunyili, Nigeria's information minister, said the government would perform the security checks the US demanded but she questioned her country's inclusion on the US list.
Although Abdulmutallab is Nigerian, she noted he had lived and studied abroad for years and said it was "unfair to discriminate against 150 million Nigerians over the behaviour of one person".
"It is outside of the shores of this country that he developed this nasty tendency to do what he tried to do," she added.
There were long lines on the first day of the new rules in Nigeria as guards wearing latex gloves combed through bags.
At the airport in the capital of Lagos, Mine Oniovosa, a 24-year-old student, said she had been told to show up more than seven hours ahead of time for a flight to Atlanta.
But at international airports in Lebanon, Syria and Libya, all on the list, there were no visible changes in screening.
"We need to be looking at all high-risk flights, irrespective of where they come from or where they are going to, and apply the appropriate measures to all passengers effectively rather than singling out a small group of nations"
Chris Yates, aviation security specialist
"Everything is the same," said an aviation official in Lebanon. "There is no extra security."
Passengers waiting to fly from Havana said thorough checks before heading to the US were nothing new, but the Cuban government denounced the security demands, with Granma, the newspaper for the ruling Communist party, calling them a "desperate directive" that was "part of the [US] anti-terrorist paranoia".
Saudi Arabia said it had placed additional security personnel at its airports.
And officials in the Netherlands announced on Monday that they would buy 60 more full-body scanners to augment the 15 already in use at Amsterdam's Schiphol airport alone.
But Chris Yates, an aviation security specialist, said wider measures were needed to improve security on US-bound airliners.
"We need to be looking at all high-risk flights, irrespective of where they come from or where they are going to, and apply the appropriate measures to all passengers effectively rather than singling out a small group of nations," he told Al Jazeera from Manchester.
"The system has to be a system of systems.
"On the one hand we are talking about technology, but we are also talking about technique as well - profiling, additional security equipment that will give us that greater capability to detect something that we really wouldn't like to see onboard."