Nakoula Basseley Nakoula, 55, was brought to court in Los Angeles still wearing his street clothes but handcuffed and shackled at the waist.
Nakoula has been under investigation into whether he violated the terms of his 2011 release from prison on a bank fraud conviction while making the film.
In refusing a request for bail, US Magistrate Judge Suzanne Segal said: "The court has a lack of trust in the defendant at this time,"
His crudely made 13-minute video was filmed in California and circulated online under several titles, including Innocence of Muslims.
The clip sparked a torrent of anti-American unrest in Egypt, Libya and dozens of other Muslim countries over the past two weeks.
The violence coincided with an attack on US diplomatic facilities in Benghazi that killed four Americans, including the US ambassador to Libya.
Nakoula, under the terms of his release from jail, has been barred from accessing the internet or using aliases without the permission of a probation officer.
He now faces eight probation violation accusations.