According to the agency, home prices showed no change month-over-month in April, down from an increase of 0.7 percent the month prior.
FHFA's index compares to the latest S&P/Case-Shiller Indices, which showed a monthly price increase of 1.1 percent among the nation's top 20 markets. Also released earlier in the week was Black Knight Financial Services' Home Price Index, which found prices were up 0.9 percent over the month.
Because FHFA's measure uses information from mortgages sold to or guaranteed by Fannie Mae and Freddie Mac, it excludes high-end jumbo sales and loans insured by the Federal Housing Administration and is often thought of as a more accurate gauge of "middle-class" home prices.
Of the nine census divisions, FHFA reports seasonally adjusted monthly price changes range from -1.3 percent in the New England division to a small 0.6 percent gain in the East South Central division. Four of the nine divisions posted declines from March.
Year-over-year, changes were positive in all divisions, ranging from 1.7 percent in the Middle Atlantic to 10.7 percent in the Pacific.
Overall, FHFA reported a 5.9 percent pickup in its index year-on-year, putting it down 6.9 percent from its April 2007 peak.