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The 39 year-old Swiss star, who has not played since losing in the semi-finals of the 2020 Australian Open, is due to make his return from a year-long layoff at the Qatar Open in Doha next week.
The Herald said Federer could play in Dubai after Doha but would then take a training break.
Federer's withdrawal is a blow to organisers of the Miami tournament, who were forced to cancel last year's event as Covid-19 chaos left sport in North America at a stand-still.
The pandemic has already impacted the 2021 calendar, delaying the Australian Open and forcing the Indian Wells tournament in California - the traditional lead-in to the Miami Open - out of its usual slot in March.
Miami is still expected to feature a strong field despite Federer's withdrawal, with world number one Novak Djokovic and 20-time Grand Slam-winner Rafael Nadal confirmed for the men's draw.
Serena Williams and newly minted Australian Open champion Naomi Osaka are also slated to appear in the women's draw.