Hagee, who operates a church in San Antonio, has drawn fire for calling the Catholic Church "the great whore" and a "false cult system."
During a campaign appearance in New Orleans Thursday, McCain called Hagee's comments "nonsense," Fox News reported.
A reporter asked if McCain would reject Hagee's endorsement.
"It's nonsense, it's nonsense, it's nonsense," McCain said. "It's nonsense. I don't have anything additional to say about that. It's nonsense."
McCain then apologized for Hagee's comments.
"I reject that categorically and I would point out there's a lot of people who have endorsed me," he said. "They support my views. That does not mean that I support -- would I consider repudiating his endorsement? I certainly condemn those parts of his remarks."
McCain said he appreciated Hagee's support for Israel "and for many of the good things that he and his church has done."
He said his association with Hagee is different from Democratic presidential hopeful Barack Obama's association with the Rev. Jeremiah Wright of Chicago, whose sermons often included rhetoric that Obama has repudiated.