The cuts were administered following the continuing poor performance of the two government-sponsored lending giants, who have both released poor second-quarter performance figures over recent days.
Share value in both firms has also diminished markedly this year.
Both the preferred stock and subordinated debt ratings for Fannie and Freddie now stand at A-, three notches below their previous level.
Additionally, Fannie's risk-to-government rating was cut to A from A+, while Freddie's was reduced to A from AA-.
Victoria Wagner, an S&P analyst, commented: "The lower risk-to-the-government rating reflects the company's worsening financial profile, which is pressured by the continued home price declines in some of its key markets, higher credit-related expenses, and capital challenges."
Between them, Fannie and Freddie hold around $2.5 trillion of debt.
This is over 50 per cent of the entire US mortgage market.