The Netherlands-flagged ship was sailing west, 96 km (60 miles) off the southern coast of Vietnam on Tuesday morning, according to data from the Marine Traffic ship tracking website.
Holland America, owned by Miami-based Carnival Corp, had said on Monday that passengers would disembark in Bangkok on Feb. 13 and that there was no reason to believe anybody on board had the virus.
"I have issued orders. Permission to dock refused," Public Health Minister Anutin Charnvirakul said in a Facebook post.