"I wish I would have basically said that it was an undeveloped site, which it is," he said Sunday on "Meet the Press."
Nagin had criticized efforts to redevelop the World Trade Center site following the Sept. 11 attacks when confronted about delays in rebuilding his city after Hurricane Katrina.
During a 60 minutes interview, CBS News correspondent Byron Pitts pointed out flood-damaged cars still on the streets of New Orleans' devastated Ninth Ward. Nagin replied, "You guys in New York can't get a hole in the ground fixed, and it's five years later. So let's be fair."
The 60 Minutes interview aired Sunday night.
Nagin told NBC he didn't mean to offend anyone.
"I meant no disrespect for anyone," he said.
"I have seen death, I have the destruction, and I was just using it as a comparison to show how difficult it is for people to rebuild after a major disaster."
He said he was sorry to the families of those who died on Sept. 11, 2001, and believe the World Trade Center site is sacred ground.