(CNN) -- The public editor for The New York Times slammed his employer Sunday in a column, saying the newspaper violated its policies by cutting MoveOn.org a deal on a controversial ad criticizing the top U.S. military commander in Iraq.
Gen. David Petraeus, the top U.S. commander in Iraq, was the target of an ad questioning his integrity.
"I think the ad violated The Times' own written standards, and the paper now says that the advertiser got a price break it was not entitled to," wrote Clark Hoyt, who analyzes the newspaper's coverage as the "readers' representative."
The group, Hoyt wrote, paid $64,575, which is the paper's "standby" rate -- meaning it cannot guarantee placement on a certain day.
The group wanted it to run on September 10, the day Gen. David Petraeus testified to Congress about the state of affairs in Iraq. The ad did run on that date, meaning MoveOn should have paid $142,083, he wrote.
In response, MoveOn announced it was never told of the error but will retroactively pay the higher rate -- even though it says the higher figure "is above the market rate paid by most" organizations.
The liberal advocacy group challenged former New York mayor and current Republican presidential hopeful Rudy Giuliani -- who paid the same lower rate for his response ad -- to follow its lead.
The New York Times said it had erred. Spokeswoman Catherine Mathis said the paper's earlier insistence that MoveOn had paid the standard rate was incorrect. Watch how the Times gives ammunition to the GOP »
"We do not, however, determine rates based on the political content of ads, and Times Company personnel did not review this ad until after the rate was accepted," she said. "Nonetheless, we made an error and were slow to respond when asked about it. We apologize."
MoveOn, in a statement, noted "there is no evidence of any kind that the error in quoting of rates was in any way based on the content of the advertisement or the identity of its sponsor."
Hoyt, while taking his paper to task, did not suggest it was the result of partisanship.
"The Times bends over backward to accommodate advocacy ads, including ads from groups with which the newspaper disagrees editorially," he wrote.
Hoyt based his assertion about an alleged violation of the paper's standards on an "an internal advertising acceptability manual" he quoted as saying, "We do not accept opinion advertisements that are attacks of a personal nature."
But he noted the executive who approved the ad "said that, while it was 'rough,' he regarded it as a comment on a public official's management of his office and therefore acceptable speech for The Times to print."
The full-page ad did not address Petraeus' personal life.
Titled "General Petraeus or General Betray Us?" the ad called Petraeus "a military man constantly at war with the facts," and cited previous quotes of his, contrasting them against quotes from independent reports and news stories.
The ad became the focus of political partisanship as soon as it was published.
During Petraeus' testimony, Republican lawmakers highlighted the ad and pressed their Democratic counterparts to condemn it, in what analysts said was a political strategy to try to force Democrats to risk losing either the support of those who admire the highly decorated general or those who agree with MoveOn.
Last week, President Bush called the ad "disgusting."
Eli Pariser, the executive director of MoveOn.org Political Action Committee, which claims to be one of the largest PAC's in the nation, responded to the president. "What's disgusting is that the president has more interest in political attacks than developing an exit strategy to get our troops out of Iraq and end this awful war," he said.
The Senate last week approved a resolution condemning the ad, 72-25. "This amendment gives our colleagues a chance to distance themselves from these despicable tactics, distance themselves from the notion that some group literally has them on a leash, like a puppet on a string," said Republican Senate Minority Leader Mitch McConnell of Kentucky.
Republicans filibustered a Democratic proposal that also condemned GOP attacks on former Sen. Max Cleland of Georgia and Sen. John Kerry of Massachusetts during his 2004 presidential campaign.
Sen. Hillary Clinton, front-runner for the Democratic presidential nomination, pointed that out Sunday.
On CNN's "Late Edition with Wolf Blitzer," she was asked about Bush's assertion that Democrats "are more afraid of irritating [groups such as Moveon.org] than they are of irritating the United States military. That was a sorry deal."
"I thought it was pretty sorry when his campaign attacked Senator Kerry's record of service, and I thought it was pretty sorry when the Republicans attacked Senator Cleland," she said. "I don't condone attacks by anyone on the patriotism and service of our military. I am an admirer of General Petraeus ... and I joined in voting for a resolution that condemned such attacks."
But, she said, some are trying to focus the nation's attention on the ad "in order to avoid having to deal with the tough questions about our policy in Iraq."
"This debate should be about the president's failed policies," Clinton said. "The Republicans are very good at coming up with political strategies, but unfortunately, they don't seem to have a very adequate grasp of military or geopolitical strategies that will forward America's standing, position, values and interests in the world." E-mail to a friend