A US citizen, Emmanuel is being held on a charge of making false statements on a passport application, Brian Roehrkasse, Justice Department spokesman, said on Friday.
He was taken into custody on Thursday night at Miami International Airport in Florida, where his flight from Trinidad had just landed, Roehrkasse said.
His father, Charles Taylor is being held at the UN-backed Special Tribunal in Sierra Leone that has charged him with war crimes.
The ex-president is accused of formenting and encouraging atrocities in civil wars in Liberia and neighbouring Sierra Leone.
Emmanuel, 29, appeared at a hearing in federal court in Miami on Friday, Roehrkasse said. He would make no further comment.
Emmanuel headed the Liberian anti-terrorist unit that was responsible for Taylor's security until he went into exile in 2003, according to an affidavit filed in federal court in Miami.
Emmanuel's name appeared on a United Nations Travel Ban list of people whose travel is supposed to be restricted, the affidavit said.
He was born in Boston in 1977, the affidavit said. Emmanuel served his father in Liberia for the duration of Taylor's rule from 1997 until August 2003, the affidavit said, citing an interview with Emmanuel's mother.