An accounting expert who raised red flags about Bernie Madoff’s Ponzi scheme has a new target: General Electric Co.

In a research report posted online Thursday, Harry Markopolos alleges the struggling conglomerate has masked the depths of its problems, resulting in inaccurate and fraudulent financial filings with regulators. The report, which numbers more than 170 pages, is a mixture of detailed financial analysis and sweeping claims.

In an interview, Mr. Markopolos said his group found GE’s insurance unit will need to bolster its reserves by $18.5 billion in cash, and he faulted the way the company is accounting for its oil-and-gas business. All told, he said, the accounting problems amount to $38 billion, or 40% of the conglomerate’s market value.

“This is market manipulation—pure and simple,” GE Chief Executive Officer Larry Culp said in a statement that was released midday Thursday. “Mr. Markopolos’s report contains false statements of fact, and these claims could have been corrected if he had checked them with GE before publishing the report.”

GE stood by its financial reporting and said the Markopolos report was produced to help short sellers by creating volatility in GE shares. Mr. Culp accused Mr. Markopolos of being motivated by personal profit rather than accurate financial analysis.