The FBI is questioning two men found carrying false IDs and carrying knives similar to those used in the terrorist attacks.
The men apparently planned to fly from Newark to Texas on Tuesday morning, but their flight was cancelled when US air space was closed.
Officials say they took a train and police stopped them in Forth Worth, suspecting they may be carrying drugs.
They were also carrying a large amount of cash, officials say.
They've been flown to New York for questioning by the FBI, who say the men may be relevant to their inquiries.
Last night US police made their first arrest in their investigation of this week's terrorist attacks, detaining a suspect in New York thought to have "crucial" information.
Mr Jim Margolin, spokesman for the FBI in New York, said the Joint Terrorist Task Force took a man into custody on a material witness warrant, which allows authorities to arrest someone considered crucial to an investigation without charging him with any crime.
A law enforcement source said the man arrested was the same person arrested on Thursday at Kennedy International Airport after showing a pilot's licence issued to his brother.
In that case, he was detained by Port Authority police and not the FBI.
It was the first big break in the investigation, code-named PENTTBOM, into the worst terrorist assault on US soil.
The FBI said it was still investigating whether more terrorists might be at large and were searching for 100 people for questioning.
Nine people arrested earlier in John F Kennedy International and LaGuardia airports in New York have been released.
AP