The 56-year-old, hosting the three-hour Sunrise breakfast programme on Sky News, had been speaking about Tuesday night’s trouble at Upton Park ahead of United’s game against West Ham, when missiles were thrown at the team bus.
Sports presenter Jacquie Beltrao said the day’s papers had been dominated by “yob culture” and were a “throwback to the Eighties”.
Mr Holmes added that it was not “the image that the English Premier League wants to portray around the world”.
He went on: “It was a dream for them on Sunday when we saw the scenes of the King Power Stadium in Leicester, but now this is going back to the Seventies and to the Eighties, and to everything you were seeing that was bad about Hillsborough, for instance.”
At the recent inquests into the deaths of the 96 fans, Liverpool supporters were exonerated over their behaviour by the jury after decades of smears.
Following angry comments on social media, Mr Holmes said: “Obviously there is no comparison between Hillsborough and the scenes we saw at West Ham last night. I apologise if anyone thought I was making that connection.”
On Twitter, he attacked critics for trying to “stir up trouble” and said the “Hillsborough familes have suffered enough without distasteful sniping like this”.