Murray on Friday tearfully declared that his chronic hip injury had not been eased by surgery a year ago.
He then emotionally revealed that he hoped to end his storied career at Wimbledon, but admitted the Australian Open may be his last event because the constant pain was so bad.
"I was disappointed and sad, a little bit shocked, to know now that we're going to lose him at some point," Federer told reporters on the eve of the year's first Grand Slam.
"But we're going to lose everybody at some point. It's just now that it's definite," he added, acknowledging that the era of the "Big Four" — himself, Novak Djokovic, Rafael Nadal and Murray was drawing inexorably to a close.
"Of course, it hits us top guys hard because we know Andy very well. We like him. He doesn't have many enemies, to be quite honest," the world number three said of the three-time Grand Slam champion and double Olympic gold medal winner.
"He's a good guy, Hall of Famer, legend. He won everything he wanted to win. Anybody would substitute their career with his. He's a great guy."
Murray has won Wimbledon twice and Federer hoped the Scot could keep playing long enough to be able to say goodbye on the famous grass courts where the Swiss maestro has won a record eight titles.
"Of course, I hope that he can play a good Australian Open and he can keep playing beyond that, really finish the way he wants to at Wimbledon. That's what I hope for him," said 20-time Grand Slam champion Federer, who begins his Australian Open title defence Monday against Denis Istomin.
"It's a tough one, but one down the road he can look back on and be incredibly proud of everything he has achieved."
Murray was the first British man to win Wimbledon in 77 years and will be remembered for battling his way to world number one in 2016 during a golden era for men's tennis alongside Federer, Djokovic and Nadal.
Murray faces a first-round clash Monday against in-form Spaniard Roberto Bautista Agut, seeded 22, who beat Djokovic on his was to winning the Qatar Open earlier this month.
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