While present-day athletes like Usain Bolt were well represented among the 361 names, Fanny Blankers-Koen was missing.
Known as the 'Flying Housewife' because she had two children, the Dutch runner became the first female to win four golds in a single Olympics at the 1948 London Games.
"With 361 tube stations and many thousands of athletes to choose from unfortunately there were always going to be some sportspeople who would not make it on to the map," said Transport for London (TfL) marketing director Chris Macleod.
"However we apologise if any offence has been caused by the omission of Fanny Blankers-Koen who was clearly a remarkable athlete. We are speaking to the publisher of the map to ensure she features in the next reprint," he said in a statement.
The Royal Dutch Athletics Federation had pointed out to Olympics chief Sebastian Coe that Blankers-Koen was worthy of a place.
Victoria Station has been renamed after sprinter Bolt while Manchester City footballer Carlos Tevez is the new Edgware Road, having won a gold medal with Argentina in 2004.
The late U.S. track and field runner Florence Griffith-Joyner also features instead of Embankment.
Alex Trickett, a former editor at BBC Sport, created the map along with his former colleague David Brooks.
"David and I used to work together in New York many years ago and spent a boring amount of time talking about sports lists and where great athletes ranked alongside each other," Trickett told Reuters. "It's what we love."
He said Blankers-Koen was mistakenly left off the map.
"She is a legend, she should be on the map," added Trickett. "There are other ones where it's a judgement call but when we saw that Fanny Blankers-Koen wasn't on the map it wasn't one to argue.
"It was a case of hands up - we messed up."
The London Olympics start on July 27.
(Additional reporting by Li-mei Hoang, editing by Tony Jimenez)
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