Despite his injury woes, a number of alterations to the ranking system have kept Federer in the top six, with Zverev one place behind him in seventh.
The ATP opted to freeze the rankings between March and August last year as a result of the disruption caused by the ongoing COVID-19 pandemic.
In October, it was announced that the leaderboard would be reflective of the previous 24 months, as opposed to the usual 12-month format.
The temporary system, which has come under fire from fans, pundits and players alike, will be in place until August.
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“I am the biggest Roger Federer fan, but he has not played for a year and is ranked higher than me,” said Zverev.
“I played a Grand Slam final, a Masters 1000 final. The system is just a disaster.”
The ranking changes have been widely criticised for carrying major implications with regards to lesser-fancied players boosting their hopes of competing at the Olympic Games in Tokyo later this year.
“Roger Federer simply changed the ranking method to protect himself, it is irresponsible and quite simply incorrect,” Hordorff told Tennisnet in December.
“In my opinion, he takes advantage of his position on the Players’ Council. It must nevertheless be said that without the change in ranking system, Roger Federer would not be in the top 50.”
Federer has only dropped three places since the changes came into effect, but would have been ranked at around 29th at the end of last year under the previous system.
The Swiss veteran admitted that he is not yet pain-free after struggling with a shoulder problem during the defeat to Basilashvili in Qatar.
“I honestly expected to feel this way,” Federer told reporters. “The whole shoulder, I feel the muscle pain around that. I didn’t expect that.
“I’d been serving the whole time but I think that comes with the pressure. In matches you just go that extra five per cent.
“Overall, the body is actually fine. I’m happy. I felt fine, a little stiff in the morning but that’s totally normal, I think.”