Issa accused Bernanke of purposefully withholding facts from the Securities and Exchange Commission (SEC) that might have scuttled a deal between the two big banks late last year.
"We think that he overstepped and used his position to support both he and [then-Treasury Secretary Henry] Paulson's attempt to make this happen," Issa said on CNBC. "There's nothing wrong with the deal as it turns out, but there is something wrong with interfering with businesses making normal due diligence and informing their stockholders."
Republicans have accused Bernanke and Paulson of threatening and pressuring Bank of America CEO Ken Lewis into accepting a deal with Merrill, whose books were stocked with toxic assets from mortgage-backed securities.
While Issa was initially reluctant to use the word "coverup," he relented, accusing Bernanke of consciously withholding facts relevant to the deal.
"We think it goes to the level of a coverup because we think that they made a conscious decision not to make these facts known," Issa said.
Issa said Bernanke should be "held accountable" for his handling of the merger.