The fans reported that a “glitch” meant their Hayya cards, the permits needed to enter Qatar, were not accepted.
One, Hywel Price from Cardiff, said he saw children in tears in the airport over the issue.
He told the BBC: “It’s hellish - there were 13 of us from Wales on that flight having the same issue, and trying to prove that we had been approved to travel, even though the app still said the permit was pending.
“People have had emails saying that their cards were valid, only to find when they get to the airport that they have been refused entry".
Mr Price said he expected hundreds more would face the same issue. Many fans have been staying in Dubai and then travelling to Doha for games.
He has since decided to watch the game in a bar with others who were not allowed onto their flights over the entry issue.
Did any Welsh fan fail to get from Dubai today due to Hayya issues? Loads finally got approved late but this whole process with day permit for Iran game has been difficult for our fans. We have informed FIFA and FAW. pic.twitter.com/7ynLdLabhy
— Fan Embassy Wales (@WeAreFSACymru) November 25, 2022
“I think this must be happening on a much wider scale than what happened to us this morning, and I expect this might continue all morning as more fans attempt to travel over to Doha for the game," he told the broadcaster.
Another fan, Kevin Morris, added online: “Mate had his approved but mine still pending. Have tickets for the match as well.”
A third affected by the issue, Wil Evans, said: “Myself and one of my mates turned away. We were due to fly at 6.20 am and in the 3 hours I spent in airport spoke to loads in the same situation.
“People on Qatar Airways allowed to fly with permits pending. Something needs to be done before England match. Total shambles.”
Fan group, Wales Football Supporters’ Association, said on Twitter: "Loads (of visas) finally got approved late but this whole process with day permit for Iran game has been difficult for our fans. We have informed Fifa and FAW [Football Association of Wales].”