Federer's ranking dropped two slots to seventh Monday, and the US Tennis Association's seedings followed the ATP standings.
Federer's record 17 Grand Slam titles include five at the US Open. He's among five former champions in the men's field, including No 1-seeded Novak Djokovic, No 2 Rafael Nadal, and No 3 Andy Murray, who won the 2012 title.
Federer was seeded No 1 at 18 consecutive Grand Slam tournaments from 2004-08.
He hadn't been seeded outside the top three at the US Open since he was 13th in 2002. The last time he was seeded fourth or worse at any major tournament was when he was No 4 at Wimbledon in 2003 - when he went on to win his first Grand Slam title.
The US Open women's seedings will be announced on Tuesday; the draw is scheduled for Thursday.
Play at the year's last major tournament starts next week.