The suspects were reportedly about to board planes to Egypt with plans to travel to Somalia to join with an extremist group there.
The Newark Star Ledger said the New Jersey men, Mohamed Hamoud Alessa 20, and Carlos Eduardo Almonte, 24, are both US citizens and quoted neighbors as saying they went to school in the United States.
"As of this moment I am only able to confirm that two arrests took place last night," an FBI spokesman said.
"Please understand due to the sensitivity of this matter this is the only information we are able to release at this time," she added.
Around the time of their arrest, both men's homes were searched by the Federal Bureau of Investigation and the federal agents carted away boxes of evidence.
Authorities told the paper the suspects had been under surveillance for some time and their circle of friends had been infiltrated by a New York City police officer who saw them prepare to travel overseas.
The men were not, however, planning an attack in the United States, authorities said.
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