The ad opens with a photo of Obama and the Rev. Jeremiah Wright together and a clip of Wright, whose incendiary comments about race have bedeviled Obama.
"He's just too extreme for North Carolina," the narrator says in the 30-second spot.
"We asked them not to run it," McCain told reporters traveling with him in Kentucky. "I'm sending them an e-mail as we speak asking them to take it down.
"I don't know why they do it. Obviously, I don't control them, but I'm making it very clear, as I have a couple of times in the past, that there's no place for that kind of campaigning, and the American people don't want it," McCain said.
McCain said the ad was described to him: "I didn't see it, and I hope that I don't see it."
Republican National Committee Chairman Mike Duncan, who accompanied McCain, said he had left a voice mail message for state party chairwoman Linda Daves asking her to pull the ad.
McCain, in an e-mail to Daves, said he will draw sharp contrasts with Democrats. "But we need not engage in political tactics that only seek to divide the American people."
Asked about the ad during an appearance in New Albany, Ind., Obama said: "My understanding is that the Republican National Committee and John McCain have both said that the ad's inappropriate. I take them at their word, and I assume that if John McCain thinks that it's an inappropriate ad, that he can get them to pull it down since he's their nominee and standard-bearer."
Democratic National Committee Chairman Howard Dean piled on, saying McCain should call the party chairwoman personally.
"If John McCain means what he says, he should call the North Carolina Republican Party chairwoman and tell her not to run this ad," Dean said. "Sending an e-mail and turning a blind eye as the state party ignores him is not leadership."
North Carolina GOP spokesman Brent Woodcox said the ad will begin running statewide on Monday, a week before the state's crucial May 6 primary. The ad actually targets gubernatorial candidates Richard Moore and Bev Perdue, Democrats who have endorsed Obama.
"We have a great relation with the RNC and we fully support John McCain for president," Woodcox said. "But this is an ad about two North Carolina candidates for governor. The ad is going to run."
Daves defended the ad, saying it "presents a question of patriotism and judgment."
"It is entirely appropriate for voters to evaluate candidates based on their past associations," Daves said.
North Carolina Democratic Party Chairman Jerry Meek said the ad is an attempt to shift attention from real issues.
"It's one thing to criticize somebody for associating with somebody else," Meek said. "But to criticize somebody for associating with somebody who associates with somebody else is ludicrous. Where does it end?"
Obama has denounced the most inflammatory of Wright's comments, but says the pastor shouldn't be judged solely on a handful of remarks. Obama has expressed admiration for the pastor, who officiated at his wedding, baptized his two daughters and inspired the title of his best-selling book, "The Audacity of Hope."
North Carolina's primary will divide 115 delegates among the Democratic presidential candidates and decide the party's nominee for governor. Polls indicate that Obama holds a comfortable lead over rival Hillary Rodham Clinton in the state.
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Associated Press writers Mike Baker in Raleigh, N.C., and Liz
Sidoti in New Albany, Ind., contributed to this report.
