Fannie Mae completed 56,816 loan modifications during the first nine months of the year with 46% involving mortgages with current loan-to-value ratios greater than 100%.

"A significant portion of our modifications pertain to loans with a mark-to-market LTV ratio greater than 100%," the GSE said in its third quarter financial report.

Fannie Mae noted that 20% of its high LTV single-family mortgages are 90-days or more past due, compared to a serious delinquency rate of 4.72% on its entire $2.8 trillion guaranteed mortgage portfolio. In the third quarter, the GSE completed 28,000 loan modifications, including a "limited number" of borrowers who qualified for the Obama administration's Home Affordable Modification Program (HAMP).

However, the GSE said a "large number" of the third quarter modifications involved borrowers "who did not qualify for modifications under the [HAMP]."

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