The 17-time Grand Slam title winner shares the same sponsor as the Indian team and on the eve of the two sides' World Cup clash in Adelaide last weekend, Federer posted a picture on his Facebook page of him admiring a blue playing jersey with the caption "Dressing up for a Gentleman's game today. #BleedBlue."
"It was more of a Nike thing to be quite honest," said the Swiss star on the eve of the Dubai Open.
"I support South Africa, and everybody knows that. The idea wasn't to spark any fire and I'm sorry if it did that."
The photograph certainly irritated Federer's legion of fans in Pakistan.
One, a student at Cambridge University in England and writing in the Express Tribune, an English language newspaper in Pakistan, claimed he had deleted all his Federer photos and taken a brief opinion poll in which ten out of 12 Pakistanis apparently felt hurt or betrayed.
His mother Lynette is from South Africa and the Roger Federer Foundation has raised large sums to help disadvantaged children in the country.
Nevertheless, Federer sought to clarify his attitude to cricket which is currently being showcased at the ongoing World Cup in Australia and New Zealand.
The Indian team, he said, he supported "a little bit."
Whether or not he followed cricket, "really depends where you are," he added.
"When I'm in America definitely not. When I'm in Europe definitely not. But then when I'm in Australia and here (in the UAE) a little bit sometimes. So it really depends where I am in the world which sport I follow."
Virat Kohli, who made a century for India in the World Cup win over Pakistan, also met Federer in Sydney in January, describing the tennis player as an "absolute legend" in a captioned picture he posted on his Twitter site.
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