Congress is in the midst of creating regulatory changes that could change the agency’s fate, Mr. Kanjorski warned the panel of official witnesses. Lawmakers want immediate candor about the handling of the Madoff matter, not generalities, he said.

But the hearing became a collision of frustrations that, at one point, prompted Mr. Kanjorski to accuse the staff members of refusing to cooperate with a branch of government that could wipe their entire agency off the regulatory map, if necessary.

Representative Gary L. Ackerman, Democrat of New York, was more blunt in his condemnation of the S.E.C. officials sitting before him: “We thought the enemy was Mr. Madoff. I think it is you.”

Mary L. Schapiro, the new chairwoman of the S.E.C., later released a letter to the subcommittee’s senior members, conceding that the hearing “cannot have been satisfactory for you.” She asked to meet with them promptly to work out “a course forward” that would both provide accountability and maintain the integrity of continuing investigations.

Image Left to right, Linda Thomsen, Andrew Donohue, Erik Sirri, Andrew Vollmer and Lori Richards of the S.E.C., and Stephen Luparello of Finra, the regulatory body. Credit... Jay Mallin/Bloomberg News

“There needs to be a full accounting, both of Mr. Madoff’s activities and why we did not detect the fraud, which we truly regret,” she said.

The hearing had opened with Mr. Markopolos telling the panel he had discovered another possible fraud, a $1 billion Ponzi scheme, that he would report to regulators on Thursday. Neither he nor his lawyers would provide any additional details.