The S.E.C. has defended its willingness to go after high-profile perpetrators with punishments beyond financial penalties. It cited a settlement with Elizabeth Holmes, the founder of Theranos, who agreed to forfeit a majority voting control over the company, and the case against Mr. Musk, whom the agency ousted as chairman of Tesla. The agency has also pointed to its hiring of a former federal prosecutor known for aggressively pursuing white-collar cases to run its New York office.

Image The S.E.C. has defended its pursuit of high-profile cases, pointing to a settlement this year with Elizabeth Holmes, the founder of Theranos. Credit... Brendan Mcdermid/Reuters

When the S.E.C. publicizes enforcement figures, it includes penalties that other government agencies have collected in related actions, and calculates them based on when the cases were resolved, not when they were filed. This method, which predates Mr. Trump, credits the S.E.C. under his administration with bringing in $1.7 billion that Petrobras, a Brazilian company, was ordered to pay to other government agencies and plaintiffs in a private lawsuit.

Tabulating penalties this way still leads to a $938 million gap between the two administrations, according to Urska Velikonja, a professor at Georgetown University Law Center who studies the S.E.C. (The Times analysis, which found a $3.1 billion gap, excluded payments to outside agencies and attributed penalties to each administration based on when a case was initiated, not settled.)

The S.E.C. disagreed with The Times’s analysis, saying that it failed to account for the natural ebb in enforcement activity at the start of an administration, and that the early months of the Trump era saw more cases filed than the beginning of the Obama era. The agency also took issue with The Times’s decision to focus on penalties, a spokeswoman said, because “the dollar amount of the penalties on their own don’t say anything about whether we’re protecting investors or enhancing market integrity.”

Some of the decline in penalties may reflect the growing skepticism over corporate penalties, particularly among the agency’s Republican commissioners. Mr. Clayton, who during his confirmation hearing said he was “100 percent committed to rooting out any fraud,” is often caught in the middle between the agency’s Republican and Democratic commissioners.

The Times also found some investigations begun under Andrew J. Ceresney, the enforcement director in the final years of Mr. Obama‘s presidency, that hit a brick wall under Mr. Trump.