The Swiss great underwent two operations last year and had only played three matches in 16 months prior to arriving in Paris
At 39, Federer is treading carefully and is understood to be saving himself for the grass court season and his bid for a ninth Wimbledon men’s singles title.
He took the decision to pull out of Roland Garros after his late-night victory over Dominik Koepfer on Saturday, sparking criticism in some quarters.
However, Murray believes Federer has earned the right to manage his body as he sees fit.
“In basketball, football etc when returning from injury players are given reduced minutes to build up their fitness,” the Scot said on Twitter.
“In tennis you don’t have that luxury of just playing a set in first match then two sets the next etc and building up that way.
“I’d argue that it’s quite risky to play multiple 4hr matches in a row in your 2nd tournament back in 18 months so to me it makes sense to be reactive based on how your body feels, length of matches etc. Sensible decision from him.”
However, Murray’s remarks provoked a mixed reaction on Twitter. One user called @WestWalesEd said: “I have to admit there is something distasteful about ‘using’ the French Open to get fit. Seems disrespectful to other players in the draw.”
Another called KeiraEve responded to Murray by tweeting: “Shocked at your response. Not much integrity there. Disappointed in Federer and you. Respect the sport, respect the tournament. Do your best. If you don’t think you can play it do a minor tournament.”
Federer, the 20-time grand slam champion, said: “After two knee surgeries and over a year of rehabilitation, it’s important that I listen to my body and make sure I don’t push myself too quickly on my road to recovery. I am thrilled to have gotten three matches under my belt. There is no greater feeling than being back on court.”
Federer had earlier defeated Denis Istomin and Marin Cilic prior to Saturday’s French Open clash with Koepfer, where he produced an error-strewn performance and needed three hours and 35 minutes to make it past the German.
Guy Forget, the French Open tournament director, said: “The Roland Garros tournament is sorry about the withdrawal of Roger Federer, who put up an incredible fight last night.
“We were all delighted to see Roger back in Paris, where he played three high-level matches. We wish him all the best for the rest of the season.”
It remains to be seen whether Federer, who turns 40 in August, will play again on the Parisian clay or whether his final memory will be of walking off an empty court at 1am.
For now, his priority is to begin training on grass ahead of next week’s ATP tournament in Halle, Germany, and then his bid for a ninth Wimbledon title.