The Securities and Exchange Commission will begin requiring admission of guilt in certain types of civil settlements, a major departure from the agency’s routine use of a boilerplate clause that allows defendants to pay fines without acknowledging liability.

SEC Chairman Mary Jo White had signaled at a recent hearing that she was reviewing the ­neither-admit-nor-deny policy, which has been harshly criticized by some judges. On Tuesday, White said some misconduct warrants wringing out an admission.

“We are going to, in certain cases, be seeking admissions going forward,” White said at a Wall Street Journal CFO Network conference. “Public accountability in particular kinds of cases can be quite important, and if you don’t get them, you litigate them.”

In an e-mail sent to the SEC staff earlier this week, the co-directors of the enforcement division said that cases in which the defendant engaged in “egregious intentional misconduct” may justify requiring an admission, as would the obstruction of an SEC investigation or “misconduct that harmed large numbers of investors.” The officials asked the agency’s staff to assess how this thinking might apply to ongoing investigations.

The SEC has previously argued that most defendants would refuse to settle if they had to admit wrongdoing. Many companies and executives would rather fight in court than admit liability and expose themselves to lawsuits, agency officials had said. The legal battles would delay compensation to harmed investors — if the SEC even wins its case.

For all those reasons, the neither-admit-nor-deny settlement model would continue to be a “major, major tool” in the SEC’s arsenal, and will be applied in most cases, White said on Tuesday. But the SEC will make exceptions, she said.

Early last year, the SEC had tweaked its settlement model by mandating admissions in cases involving defendants who had already entered guilty pleas in related criminal settlements.

Fierce debate about the boilerplate language began about two years ago, when Judge Jed S. Rakoff rejected a $285 million settlement that the SEC negotiated with Citigroup, in part because the deal included neither-admit-nor-deny language. The SEC has appealed, and the case is pending before a panel of the U.S. Second Circuit Court of Appeals.

Citigroup had agreed to settle allegations that it misled investors into buying deteriorating assets in a weakening housing market. But Rakoff ruled that because Citigroup did not admit or deny wrongdoing, he had no way of knowing if the settlement size he was asked to approve was too little or too much.

Since then, a handful of other judges have voiced their discomfort with allowing defendants to pay fines without admitting liability.

In April, U.S. District Judge Victor Marrero in Manhattan held off on final approval of a $602 million insider trading settlement between the SEC and SAC Capital Advisors because he questioned whether SAC should have to acknowledge wrongdoing.

Marrero said he would only approve the deal if it complies with the court’s findings in the Citigroup appeal, which should determine whether Rakoff exceeded his authority in rejecting the Citigroup deal.

“Under the circumstances, the most prudent course the Court sees open to it would be to approve the settlement subject to a condition that it would become final upon a definitive determination in the Citigroup appeal,” Marrero wrote in his 34-page decision.

Earlier this year, a federal judge in Colorado initially refused to approve a settlement involving an alleged $16 million Ponzi scheme run by Bridge Premium Finance, citing the SEC’s failure to get an admission of wrongdoing from that company.

And in December 2011, a federal judge in Wisconsin scrutinized a settlement between the SEC and Koss Corp. and cited Rakoff’s decision. Officials at the Milwaukee-based firm were accused of accounting fraud, but did not admit or deny misdeeds.

In both cases, the judges eventually approved the settlements.

All these cases preceded White’s arrival at the SEC. But on Tuesday, White said that the SEC has made “good use” of the neither-admit-nor-deny model. In the e-mail to the agency’s staff, the heads of the SEC’s enforcement division — George Canellos and Andrew Ceresney — said they would “continue to strongly defend our discretion to reach such settlements in response to inquiries from courts.”