Ferguson's comments that Webb was the "best man for the job" prior to last weekend's game with Chelsea were largely innocuous but an FA statement said they contravened rules about commenting on referees in the build-up to matches.
Ferguson, who has only recently completed a five-match touchline ban for his remarks about referee Martin Atkinson after United's defeat at Chelsea in March, has until 4pm (1500GMT) on May 16 to respond.
In comments to the media ahead of last Sunday's game with Chelsea, won 2-1 by United, Ferguson had welcomed the appointment of Webb for the match, while stating he hoped his team enjoyed "a little bit of luck" from officials.
"He's definitely the best referee in the country, there's no doubt about that," Ferguson said of Webb, who refereed last year's World Cup final between Spain and Holland.
"We are getting the best referee and we hope it's our turn for a little bit of luck," Ferguson added.
News of the fresh disciplinary proceedings against Ferguson came as United prepared to clinch a record 19th league title against Blackburn Rovers on Saturday.
Ferguson, meanwhile, said on Friday he was unconcerned by the fact that United will not be presented with the Premier League trophy if they secure the title, with Manchester City facing Stoke in the FA Cup final on the same day.
"I think they would have planned it to be presented with the cup at our own stadium anyway, with the final game at home," Ferguson said.
"I'm not sure what the mechanics would have been if the FA Cup final wasn't on. But because of the European (Champions League) final, which is two weeks later, the FA Cup final has been brought forward.
"So we know it's a big game for us. And even though we have been disappointed with our away form this season, now is not a time to analyse it. We have to get over the line first.
"But there's no question our home form has won us the league. If we do, it has been down to that. It's been fantastic and I don't think anyone in Europe has that kind of record at home. Hopefully we will get the result now."
Ferguson believes his double-chasing squad are reaching their peak in the closing stages of the season thanks to the return of his injured players.
The Scot has a fully-fit squad to choose from and he says he has benefited from such a luxury.
"What's helped us lately is the freshness of players coming back," he said.
"(Antonio) Valencia and Ji-Sung Park are two that have come back. Anderson is another. There has been a lot of added impetus at an important time.
"Valencia's form has been terrific, Park has been doing a magnificent job and Anderson has been doing really well. It's been a real boost to us."
Among those yet to make a comeback is Darren Fletcher. The Scottish midfielder, who missed 12 games with a virus, is targeting a place in the Champions League final against Barcelona at Wembley later this month.
"Fletcher has played for the reserves and hopefully those kind of games will bring him to the level we need in the final of the European Cup," he said.
"We have another reserve game in midweek and Blackpool next Sunday.
"We have Gary Neville's testimonial game (against Juventus), so there are opportunities to increase his work rate and fitness for a particular game like a European final.
"We have to give him a chance. He is back training every day. He is over the virus he had. It's a matter of getting that strength and speed to his game.
"We have some games to do that. He will go very close. He has the application and desire to do it and hopefully we can get him there."
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