The 59-year-old was heard telling his co-host: “I don’t know exactly how au fait with the rules Kate is, but I assume she must have been struggling a bit in the last 20 minutes.”
John added: “And she wasn’t alone.”
Angry viewers took to Twitter to criticise the commentator, branding his remarks sexist and suggesting he retire.
One posted: “So once again John Inverdale puts himself up for this year’s Foot in Mouth award #johninverdale #sexist #timetogo.”
Another commented: “Once again shameful sexism from John Inverdale @BBCSport #sixnations #needstogo.”
A third tweeted: “Someone tell me that there is a reason other than HRH Kate being female that would cause John Inverdale to doubt her knowledge.”
A BBC spokesperson told Express.co.uk: “John was saying that many would have been bemused by the nature of the protracted end of the match.”
John was involved in another sexism row in 2013 with French tennis player Marion Bartoli.
He asked BBC Radio 5 listeners: “Do you think Bartoli’s dad told her when she was little, ‘You’re never going to be a looker? You’ll never be a Sharapova, so you have to be scrappy and fight.”
John later blamed his comments on hayfever as the BBC apologised, saying: “We accept this was insensitive and for that we apologise.”
Express.co.uk has contacted a representative for John Inverdale for comment.