If investors were scratching their heads over a statement Wednesday from Fannie Mae's ( FNM) federal regulator, they aren't anymore.

Apparently discomfited by some garden-variety spin, the Office of Federal Housing Enterprise Oversight took the unusual step Thursday of accusing Fannie of making misleading statements to the press. It then laid out some specific and troubling concerns about the mortgage giant's accounting policies, several of which were foreseen in columns on Thursday and previously by Real Money's Peter Eavis.

The storm blew up Wednesday when OFHEO raised the prospect that Fannie might have to restate prior earnings and recalculate capital levels after what is normally a routine quarterly review. Fannie pooh-poohed the remarks, saying OFHEO "obviously has not reached any conclusions."

"We are not aware of anything that backs the assertion that there may be a need for us to restate our financial results," the company told The Washington Post. "If anyone has evidence to the contrary, they should share it with us directly. Otherwise, it is irresponsible to speculate on this topic and affect markets where billions of dollars of securities are traded every day."

That got the agency's dander up.

"If OFHEO has reason to believe that the capital calculations may be subject to change, we have an obligation to caveat the capital information with such a disclosure," the agency said. Far from being reiterated boilerplate, OFHEO said, its comments Wednesday "for the first time noted the possibility of a Fannie Mae restatement and a subsequent effect on the capital calculations.

"A statement made by Fannie Mae to The Washington Post concerning OFHEO's investigation was inaccurate and misleading," the agency said.

So what in Fannie's earnings statements is OFHEO specifically worried about?

"OFHEO's investigation of Fannie Mae's accounting policies and practices is proceeding with a broad review of all accounting matters but has also been intensely focused on several specific issues," the agency said. "One involves Fannie Mae's accounting for impairments. Our review of this particular matter, while not concluded, has led to concerns that Fannie Mae may not have applied the proper accounting guidance in this area."

As noted on Real Money Thursday morning, Fannie was carrying $8 billion of bonds backed by mobile-home loans on its books at the end of last year. About 70% of those were originally serviced by Conseco Finance, a company whose 2003 bankruptcy resulted in the bonds having a lesser claim on the payments from the underlying loans.

Fannie has taken writedowns on the bonds totaling just over $200 million at the end of last year, a level Eavis calculated could be as much as five times too small.

OFHEO mentioned the securities by name in its statement Thursday.

A restatement "could affect not only the company's manufactured housing portfolio but other assets as well. The impact of this possible misapplication of GAAP on Fannie Mae's financial statements is under examination," the agency said.

Fannie's shares shrugged the whole thing off, recently rising 55 cents, or 0.7%, to $74.90.