General Electric's CEO said the accusations of fraud by Madoff whistleblower Harry Markopolos are false, and driven by market manipulation.

"GE will always take any allegation of financial misconduct seriously. But this is market manipulation – pure and simple," Lawrence Culp, chairman and chief executive officer of GE said in a statement. "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."

Culp said the fact that Markopolos never talked to company officials before publishing the report "goes to show that he is not interested in accurate financial analysis, but solely in generating downward volatility in GE stock so that he and his undisclosed hedge fund partner can personally profit."

Markopolos on Thursday targeted GE in a 175-page report, accusing the conglomerate of issuing fraudulent financial statements to hide the extent of its accounting problems.

A U.S. hedge fund, that Markopolos wouldn't name, paid Markopolos to research and publish his report, and Markopolos told CNBC that he was getting a "decent percentage" of profits that the hedge fund would make from betting against GE.

Leslie Seidman, a GE board director and chair of its audit committee, also accused Markopolos of inaccuracies.

"The report contains numerous novel interpretations and downright mistakes about the actual accounting requirements, making his conclusions about GE's reporting questionable at best," she said in a statement. "In his own words, he stands to personally financially benefit from today's significant market reaction to his report, and he is selectively front-running widely reported regulatory processes and rigorous investigations without the benefit of any access to GE's books and records."