Kim Davis, who has refused to yield despite a US Supreme Court ruling upholding the right of gays to marry, told the court it was against her Christian beliefs to issue licenses to same-sex couples.
"My conscience will not allow me," she was quoted as saying by ABC News.
She was removed from the courtroom by deputy marshalls, the report said. US District Judge David Bunning ordered her jailed, saying she could be released if she complies with the order to resume issuing licenses, according to ABC.
Davis had filed suit in federal court, arguing that her religious beliefs should exempt her from the ruling. A federal judge however disagreed.
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Davis appealed the ruling to the Supreme Court and sought an emergency stay, but the court rejected her motion.
The case has drawn national television coverage with footage of confrontations between Davis and gay couples seeking marriage licenses.
Kentucky Governor Steve Beshear in July ordered all county clerks to obey the Supreme Court's ruling and allow same-sex marriages to take place, or resign.