Nakoula, also known as "Sam Bacile," has been in hiding since the film's release in the Arab world more than two weeks ago when it was broadcast over satellite TV. The 55-year-old has been on probation for a 2010 federal check fraud conviction and served a 21-month prison sentence.
Under terms of his probation, he was not to use computers or the Internet for five years without approval from his probation officer.
Nakoula was taken into custody Thursday by U.S. Marshals, according to Justice Department officials.
A U.S. District Court hearing was scheduled for Nakoula on Thursday afternoon. It was closed to media and the public. Nakoula was to appear remotely at the preliminary hearing.
Eight allegations of violating terms of supervising release were cited at the hearing.
Nakoula's defense attorney requested his release citing danger to Nakoula if he's detained. U.S. Central District Chief Magistrate Judge Suzanne Segal denied the request and ordered him held without bail, saying Nakoula is a flight risk and poses a danger to society.
The judge asked Nakoula if that was his real name. He said since 2002 his real name is Mark Baciles Ussef. The judge then determined to change the court records to reflect "Mark" as the defendant's name instead of "Nakoula."
According to Justice officials, the probation violations involve Nakoula's use of aliases and restrictions on the Internet that were part of his probation.
The president of the Muslim Public Affair Council said Nakoula was a fraud from the very beginning.
"That criminal background basically underscored how he had a checkered past, and now justice caught up with him today," said Salam Al-Marayati.
The 14-minute film titled "Innocence of Muslims" has been cited as being responsible for mob violence in Tunisia, Libya and Egypt and elsewhere in the Arab world. A terrorist attack killed the American ambassador in the Libyan city of Benghazi on September 11 of this year.
Susan Rice, U.S. Ambassador to the United Nations, said on September 16 the attack was a spontaneous reaction to the video. US Defense Secretary Leon Panetta said Thursday it was planned attack by terrorists.
Some of the actors in the film claim they were duped. They say when the film was shot it was titled "Desert Warrior" and there were no references to Islam. They contend that the film was later edited to include suggestions the prophet Muhammad was a fraud, a womanizer and a pedophile.
The film was reportedly uploaded to the Internet in July 2012.
At least one actor in the film went to court to request the video being taken down from YouTube. That request was denied in the U.S.
No date has been set for Nakoula's next hearing. If convicted, he faces up to 24 months in federal prison.
CORRECTION: It was incorrectly reported that Nakoula was arrested for a parole violation. It was a probation violation. The information has been updated.
The Associated Press contributed to this report.