Federer pulled out of his title showdown with Djokovic at the ATP Tour finals yesterday just before the match was due to begin.
The world number two now faces a race against time to be fit for the Davis Cup final against France, which gets underway in Lille on Friday.
The 33-year-old aggravated a back problem, which has troubled him at various times this year, during a gruelling three-set victory over Davis Cup team-mate Stan Wawrinka on Friday.
"I spoke to him and it's a question mark for the Davis Cup final. He doesn't know yet," said Djokovic.
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"The stats are saying clearly that he is one of those players that would compete and would always fight if he can. He has had, what, three retirements in his entire career.
"I don't think he was calculating and trying to save his body for Davis Cup final.
"I'm sure that wasn't the case. This is probably one of the biggest matches of the year for him. I'm sure if he could have, he would be on the court."