The Federal Housing Administration (FHA) , facing a $16.3 billion deficit, will increase mortgage fees next year. FHA, the primary source of funding for first-time home buyers and those with modest incomes, said it would raise the premiums it charges on loans it guarantees by 10 basis points, adding, on average, about $13 per month to a borrower's cost.

The FHA's role in the mortgage market has expanded rapidly since the U.S. housing bubble burst. It now insures about 1.2 million mortgages, supporting about 15 percent of all U.S. home loans, up from 5 percent in 2006.  It is often the preferred loan choice among first time homebuyers as it gives them a lower down payment option compared to conventional financing through Fannie Mae or Freddie Mac.

This round of fee increases could just be the first step in higher costs for FHA insured mortgages, so it might be the right time to take advantage of the lower rates and fees that are in place now before they go up.