Anas al-Libi, a computer expert who had a USD 5 million bounty on his head as an alleged member of Al-Qaeda, arrived in New York at the weekend, a prosecutor said.
The 49-year-old was indicted in the city in 2000, accused of conspiring in the bombing of the US embassy in Kenya that killed 213 people on August 7 1998.
Another 5,000 people were wounded in the attack. A near simultaneous truck bomb outside the US mission in Tanzania killed a further 11 people and wounded 70 more.
The terror group was not stopped and three years later carried out the 9/11 attacks that killed 3,000 people and brought down New York's World Trade Center.
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New York South District attorney Preet Bharara said in a statement that Libi had been "transferred to law enforcement custody this weekend".
"The government expects that he will be presented before a judicial officer tomorrow," he added.
Libi was snatched from the streets of the Libyan capital by US commandos on October 5.
He was then held and interrogated onboard the USS San Antonio, an amphibious American transport ship in the Mediterranean.
The suspect's given name is Nazih Abdul Hamed al-Raghie and he was on the FBI's most wanted list over his alleged role in the East Africa embassy attacks.
The married father-of-four is accused of conspiracy to murder, kidnap and maim Americans and of plotting to maliciously damage and destroy US property.
The New York indictment of him and 20 other presumed Al-Qaeda lieutenants refers to him in direct connection only to the US embassy bombing in Kenya.
It accuses Libi in 1993 of discussing possible attacks against the US embassy in Nairobi, and of surveilling the diplomatic mission.
US President Barack Obama said last week Libi "planned and helped to execute a plot that killed hundreds of people, a whole lot of Americans."
"We have strong evidence of that. And he will be brought to justice," Obama added.
Libi's capture embarrassed Libya and put it under pressure from its critics, notably former rebel groups from the 2011 revolt that ousted dictator Moamer Kadhafi.