Murray, Wimbledon victor in 2013 and 2016, has not played since crashing out at the quarter-finals stage at SW19 in July and will now miss the last Grand Slam of the year.
"Had the issue with the hip over what's actually been since my match with Stan in Paris", Murray, 30, told reporters in a previously scheduled news conference.
"I obviously spoke to a lot of hip specialists".
Murray, who will miss a slam for the first time since the French Open in 2013, said: "If I get myself fit and healthy, there is no reason why I can't (come back at the same level)".
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The 30-year-old World No.2, victor of the 2012 event, is the fifth player ranked in the ATP Tour's top 11 to withdraw from Flushing Meadows after Serbian two-time champion Novak Djokovic, Swiss defending champion Stan Wawrinka, Japan's Kei Nishikori and Canada's Milos Raonic.
"I certainly wouldn't have been hurting myself more by trying to play". That's something that I'll sit down and decide with my team. "But I'll decide on that in the next couple of days, for sure".
If Murray had pulled out of the field anytime before the draw was conducted Thursday, then Federer would have moved up to the No. 2 seeding and automatically would be in the bottom half of the bracket, setting up the possibility of a final between him and Nadal.
Querrey, seeded 17th for the US Open, moves from his spot into the draw into the place vacated by Cilic, thus putting him against France's Gilles Simon in the first round in the same quarter of the draw as German fourth seed Alexander Zverev.
The lucky loser is Lukas Lacko (that nearly rhymes).
Add in 2016 Wimbledon runner-up Milos Raonic, who has a problem with his left wrist, and Murray, and now five of the top 11 men in this week's ATP rankings will be absent. And now, with Murray out, the top half of the draw is definitely the more challenging one.