The results of FHA’s annual audit sent a shock wave through the nation’s housing community Friday afternoon as even agency officials could not confirm that the higher borrowing costs it will charge borrowers will enough to cover losses.

The FHA reported on Friday that its annual audit shows that even if it stopped making any new loans immediately, the agency doesn’t have enough in reserve to cover expected losses on loans already in its portfolio. The result would lead to a $16.3 billion net worth deficit.

The agency announced it will raise premiums and sell delinquent loans as it seeks to avoid taking aid from taxpayers for the first time in its 78- year history, but when asked whether those steps will be enough to overcome the deficit, FHA Acting Commissioner Carol Galante declined to speculate on whether these measures would be enough to keep the agency from seeking Treasury assistance.

“At this point in time, it’s literally impossible to say whether we will or won’t need a draw,” she said during a briefing for reporters in Washington. “We are doing this to increase the likelihood that we will not.” More than 17 percent of all FHA loans were delinquent in September. The agency has lost $70 billion on loans it insured from fiscal years 2007 through 2009.

Most of the FHA’s price increases will go into effect in January. The annual premium FHA charges borrowers in return for guaranteeing loans will rise by 10 basis points on new mortgages, an average cost of about $13 per month for borrowers. The agency also will no longer allow some borrowers to stop paying premiums after 10 years. FHA will also provide deeper levels of payment relief for borrowers who receive loan modifications to avert foreclosure.

In addition, FHA will expand short sales for defaulting borrowers and continue auctioning off at least 10,000 delinquent loans every quarter, urging investors who buy them to take steps to keep families in their homes.

The premium increase comes on top of a significant hike in mortgage insurance premiums and tighter credit standards enacted late last year and earlier this year. The higher costs are driving borrowers who can qualify to use conventional financing, which may be accelerating the deterioration of the quality its portfolio.

Earlier this year, FHA raised upfront mortgage insurance premiums to 1.75 percent of the amount borrowed, due at closing and raised annual mortgage insurance premiums to as high as 1.25 percent a per year. FHA also refused to lend to borrowers with FICO scores below 530 and instituted a 10 percent down payment requirement for those with scores between 530 and 580.

Following implementation of the new policies, use of FHA loans declined. In January, FHA transactions accounted for 27.3 percent of all home purchase transactions. FHA-financed transactions were only 25.9 percent in August, according to the Campbell Surveys/Inside Mortgage Finance Housing Pulse. Ellie Mae also reported that the FHA share of mortgage originations declined, from 29 percent in August 2011 to 17 percent in September 2012. During the same period, conventional mortgages increased their market share of new from 61 to 72 percent.

Higher borrowing costs will affect first-time buyers more than others. FHA mortgages were used by 46 percent of first-time buyers in 2011. In September, the media FICO score of FHA borrowers was 701, according to Ellie Mae, whose software platform processes about 20 percent of all U.S. mortgage originations.

“Conventional mortgages are making a comeback while FHA mortgages are not,” said Thomas Popik, research director for Campbell Surveys in September. “Reasons for the growth in conventional mortgages include low rates, increased underwriting of high LTV mortgages by private mortgage insurers, and a price structure including insurance premiums that is cheaper than the FHA alternative.”

Housing organizations across the spectrum issued statements of concern about the audit. “While there is no doubt that the housing finance system needs to be reformed, the contributions that the FHA has made during this economic downturn underscore the need for a government backstop for both the primary and secondary mortgage markets. In times of crisis, private financial institutions have fled the marketplace and consistently failed to step up to the plate. Without government support for home purchasing and refinancing, the nation’s mortgage markets will grind to a halt, throwing the economy back into recession,” said Barry Rutenberg, chairman of the National Association of Home Builders (NAHB).

Mike Calhoun, president of the Center for Responsible Lending, said, “FHA has already instituted changes so that its current and more recent loans are projected to generate a profit. Those safeguards, along with the additional changes FHA announced today, should produce the additional revenue that will enable FHA to operate without a subsidy from taxpayers. Further restrictions, however, would undercut the ability of FHA to fulfill its mission.”

Said Debra W. Still, CMB, Chairman of the Mortgage Bankers Association (MBA): “While everyone had hoped for a better report, the news that the Fund has gone negative is not wholly unexpected, as last year’s report predicted there was a 50 percent likelihood this would occur. The characteristics and stresses on FHA’s pre-2010 books of business continue to be the source of losses, while books from 2010 onward are performing well.

“The good news is that the steps that FHA has taken to better manage its risk in recent years have succeeded in vastly improving loan performance on more recent vintages. The industry welcomed many of those changes and believes that policymakers can take further steps that would stabilize FHA single family programs, starting with a rigorous look at the data driving the actuarial results and an open, robust discussion over the future of the government’s role in housing finance.”

“Given the significant role that housing plays in the economy, policymakers need to take a long-term, holistic approach to housing finance reform and carefully gauge how it affects other efforts under way to get the nation’s fiscal house in order and achieve long-term economic growth.”