The Spaniard has pulled out of the Paris event because of an abdominal injury, the BBC reports, and is unsure if he will play in the season finale in London from 11-18 November.
The 32-year-old withdrew ahead of his first match at the ongoing tournament on Wednesday, meaning that Novak Djokovic of Serbia will return to the top of the ATP Rankings in men singles on 5 November.
This time it wasn't the troublesome right knee which had sidelined him since the U.S. Open semifinals in early September, but rather an abdominal injury which just crept up on him.
Second seeded Djokovic has secured the world No. 1 spot following Spanish tennis great Rafael Nadal's retirement on Wednesday due to abdominal problems.
"I feel like it's better for me to play matches rather than practice", Federer said.
"But I haven't been really reflecting on that and I haven't been really focusing on that too much because it's the middle of the week. And, of course, I'm very, very happy and proud about it", said Djokovic.
But Djokovic has completely turned his form around, winning four of the last five tournaments he has entered, including Wimbledon, the U.S. Open and most recently the Shanghai Masters.
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"It's always fun to play him".
Filip Krajinovic, last year's runner-up in Paris, slid to a first-round defeat by Karen Khachanov that will send the Serb spiralling down the rankings. For Nadal it means delaying his long-awaited comeback from injury which has kept him sidelined since the US Open.
"Hopefully I can travel with him a bit more next year, and for sure we're going to try to spend a lot more time together in the upcoming weekends and months".
Djokovic established his quarterfinal clash with fifth-seeded Marin Cilic.
If he wins against Nishikori, he could face Novak Djokovic in the semifinals - but Federer is thinking more about winning the ATP Finals. The American got past lucky loser Malek Jaziri, but will now run into Dominic Thiem.
Nishikori crucially broke the Frenchman at 5-5 in the first set and 3-3 in the second to set up the win. Elsewhere, German fourth seed Alexander Zverev, playing his 70th match of the season, defeated Frances Tiafoe of the United States 6-4, 6-4 while defending champion Jack Sock put out Richard Gasquet 6-3, 6-3.