The Rev. Michael Pfleger, a Chicago activist, also apologized for last Sunday's sermon at Obama's church, in which he said Clinton's eyes welled with tears before the New Hampshire primary because she felt "entitled" to the Democratic nomination and because "there's a black man stealing my show."
In video circulating on the Internet, Pfleger said the former first lady expected to win the nomination before Obama's sudden popularity.
"She just always thought that, 'This is mine. I'm Bill's wife. I'm white.' ... And then, out of nowhere, came 'Hey, I'm Barack Obama." And she said, 'Oh damn, where did you come from? I'm white. I'm entitled. There's a black man stealing my show,"' Pfleger said at Trinity United Church of Christ.
He then went on to parody Clinton, sobbing and wiping his face with a handkerchief.
"She wasn't the only one crying," he said. "There was a whole lot of white people crying."
Obama won the Iowa caucuses, the first contest of the nominating season, in January. Days later, Clinton's eyes brimmed with tears and her voice broke as she talked with New Hampshire voters on the eve of the primary, which she won.
Obama said he was "deeply disappointed" by Pfleger's comments.
"As I have traveled this country, I've been impressed not by what divides us, but by all that that unites us," he said in a statement. "That is why I am deeply disappointed in Father Pfleger's divisive, backward-looking rhetoric, which doesn't reflect the country I see or the desire of people across America to come together in common cause."
This latest distraction comes as Democratic party leaders are pushing for a quick end to the campaign by urging uncommitted delegates to make up their mind, reports CBS News chief White House correspondent Jim Axelrod.
Pfleger, the white pastor of predominantly black Saint Sabina Roman Catholic Church on the city's Southwest side, said he regretted his choice of words.
"These words are inconsistent with Senator Obama's life and message and I am deeply sorry if they offended Senator Clinton or anyone else who saw them," Pfleger said.
Clinton's campaign denounced Pfleger's comments.
"Divisive and hateful language like that is totally counterproductive in our efforts to bring our party together and have no place at the pulpit or in our politics," the campaign said in a statement. "We are disappointed that Senator Obama didn't specifically reject Father's Pfleger's despicable comments about Senator Clinton, and assume he will do so."
In March, Pfleger invited Obama's embattled former pastor, the Rev. Jeremiah Wright, to speak at Saint Sabina, embracing Wright in the church.
Obama recently broke with Wright, who had been his longtime pastor, after video of his sermons blaming U.S. policies for the Sept. 11 attacks and his calls of "God damn America" became fixtures on the Internet and cable news networks and created a political problem for the candidate.
Pfleger, known locally as a community activist and organizer, was arrested in June 2007 with the Rev. Jesse Jackson during a protest outside of a south suburban Chicago gun shop. The criminal trespass charges were later dropped.
He also has hosted Louis Farrakhan, the controversial leader of the Nation of Islam, at St. Sabina and has called him "a gift from God to a sick, sick world."
The head of the Roman Catholic Archdiocese of Chicago said Pfleger's comments "are both partisan and amount to a personal attack."
Cardinal Francis George issued a statement in which he says he deeply regrets the remarks Pfleger made about Clinton during a gathering at Trinity United Church of Christ last Sunday.
George says Pfleger has promised him that he won't do any campaigning or publicly mention any candidate by name from now on.
Republican presumptive nominee also weighed in on the flap, reports CBS News reporter John Bentley.
"I have known Sen. Clinton for a long time," McCain said. "I respect her, and I think that kind of language and that kind of treatment of Sen. Clinton is unwarranted, uncalled for, and disgraceful."