A formal complaint was made to the match delegate, Nick Cusack, whose report has been passed to the FA. Clattenburg's own version of events, which contains an 'extraordinary incident report', has also been passed to the game's governing body. These are submitted by referees on matters that may require FA intervention.
That process looks set to involve Clattenburg, Mikel and Mata all being interviewed by FA compliance officers, who are likely to speak to other potential witnesses.
Those could include other Chelsea and Manchester United players and will almost certainly see Clattenburg's assistants and fourth official asked to provide evidence.
Clattenburg, Michael McDonough, Simon Long and Michael Jones all wore microphones and earpieces yesterday, although their conversations were not recorded.
In the mean time, the Professional Game Match Officials' Board has decided that Clattenburg should be stood down from the next round of Premier League matches due to the intense scrutiny that he would inevitably attract.
"Professional Game Match Officials believe that, with any football match, the focus should not be on the officials but on the players and the game itself," said a statement.
"Mark Clattenburg is one of the elite referees in world football and, in these circumstances, the intense level of scrutiny would detract from the match and be unfair to the clubs and the supporters of both sides."
The FA has also confirmed that an investigation will be launched into Chelsea's allegations.
"The FA has begun an investigation relating to allegations made following Sunday's fixture at Stamford Bridge between Chelsea and Manchester United (Sunday 28 October 2012),” said a statement on the FA website.
The referees' union, Prospect, meanwhile, has pledged its "full support" to Clattenburg.
"Prospect is committed to helping to eradicate racism in football and in society generally," said a statement.
"In the context of that commitment, Prospect is offering full support to Mark Clattenburg in relation to the allegations made against him.
"It is now important that the allegations are fully investigated through the proper process as quickly as possible."
Metropolitan Police commissioner Bernard Hogan Howe said the force had not yet received a complaint about the alleged comments.
He told reporters: "If we hear of any report, we will look into it."
Former Premier League referee Jeff Winter, who retired shortly before Clattenburg became a member of the top flight's Select Group, believes the official is doomed if he is proven to have used "racial insults" towards a player.
Luis Suarez and John Terry received respective eight and four-match suspensions this year for racially abusing Patrice Evra and Anton Ferdinand.
But Winter, who refereed for over 25 years, feels Clattenburg will be kicked out of the game if found guilty.
"If a match official has used racial insults or language to a player then he's for the high jump," Winter said.
"He won't be getting a four-match or an eight-match ban, it'll probably be the end of his career, but that is if indeed he did say anything."
He added: "I feel it very unlikely that Mark Clattenburg would be allowed to referee until it's dealt with so we certainly don't want this going on for weeks and months."