"I have disagreements with other presidential candidates," said Haley, later adding, "Marco Rubio believes in amnesty, which I don't. There's lots of things."
Later, in an interview with Fox News, she walked it back.
"I'm against his Gang of Eight bill. He is not for amnesty, but I was against his Gang of Eight bill," she said, referencing the bipartisan group Rubio once belonged to that pushed comprehensive immigration reform legislation.
Moments after that, Haley elaborated.
"It's been a long couple of days," she said. "What I said was that I didn't agree with him -- I meant what I didn't agree with him was on the Gang of Eight bill. I said that he wasn't for amnesty. That's not what I meant. What I meant was that he supported the Gang of Eight bill and I did not."
Spokesmen for Rubio and Haley did not immediately respond to requests for comment on whether the Rubio campaign and Haley's office were in touch after Haley's initial comment.
Haley's remarks complicates matters for Rubio in the state that goes third in the nominating process for several reasons.
They called attention to a sensitive area for Rubio, who has come under increasing attacks from GOP rivals and their supporters charging that Rubio supports "amnesty" because he once pushed comprehensive immigration reform or because he currently supports a path to citizenship for undocumented immigrants. Rubio has pushed back on the campaign trail, saying frequently lately that he doesn't support "amnesty."
South Carolina is a state where Rubio is competing hard. It also happens to be the state hosting the next televised Republican debate on Thursday night.
Haley is neutral in the Republican primary and she is an emerging national figure. What she says about the campaign attracts attention -- inside and outside South Carolina.
Even though she walked back her remarks, she gave fodder to Rubio's opponents, who can now say that the state's neutral Republican governor takes issue with at least part of Rubio's record on immigration. And they can raise questions about why she said he supports "amnesty" in the first place.