(CNN) -- English football has been plagued by racism scandals in the past year, and now its ruling body must deal with what is thought to be the first case of racial abuse by a Premier League referee.
League leaders Chelsea made a complaint over "inappropriate language" used by ref Mark Clattenburg during Sunday's controversial 3-2 home defeat by Manchester United.
Chelsea's complaint focused on comments made to two of its players in two separate incidents.
Clattenburg had already infuriated the European champions by sending off two of their players, dismissing Fernando Torres for diving even though he had been fouled and then allowing United's winning goal to stand even though television replays showed it appeared to be offside.
With the issue of racism in English football under intense scrutiny, and following in the wake of Chelsea's own problems with captain John Terry's ban for racially abusing an opponent, the allegations against Clattenburg come at a time when the Football Association is under pressure to be seen to be taking a strong stance.
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Longest match in EPL history
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"I can't think of any previous such incident in the professional game off the top of my head," an FA spokesman told CNN.
"In grassroots football, yes, I can recall incidents but in the professional game I would have to check the record books."
The FA said on Monday they had launched an investigation into the allegations, while Clattenburg has welcomed "the opportunity for the facts to be established."
"We have lodged a complaint to the Premier League match delegate with regard to inappropriate language used by the referee and directed at two of our players in two separate incidents during (the) match," Chelsea said in a statement said on Sunday.
"The match delegate will pass the complaint to the Football Association. We will make no further comment at this time."
British media have reported that one of the players involved was Chelsea's Nigeria international John Obi Mikel.
For the past year, the Blues have been at the heart of a racism row after an incident involving Terry and Queens Park Rangers defender Anton Ferdinand during a Premier League match in October 2011.
The FA found Terry guilty of racially abusing Ferdinand, even though a court had earlier cleared the former England captain.
The FA -- which requires a lower burden of proof than an English criminal court -- barred the 31-year-old for four games for the incident and also fined him £220,000.
Terry missed Sunday's Stamford Bridge clash with second-placed United, who now trail Chelsea by just a point, as he served the second game of his ban.
Read: Terry decides against appealing FA racism verdict
Chelsea's complaint means the FA will now have questions to answer after an allegation against one of its top referees.
The body which represents Premier League referees -- the Professional Game Match Officials (PGMO) -- said it is aware of the allegations and "they are being treated with the utmost seriousness."
"Mark will co-operate fully and welcomes the opportunity for the facts to be established," it said in a statement.
All four match officials -- the referee, his two assistants and the fourth official -- wore microphones and ear pieces that allowed them to hear what each other was saying throughout the match.
But under the guidelines of football's world governing body FIFA, what is said between them is not recorded.
The allegations against Clattenburg come at a time when the FA is already under fire from several black players, who feel that the punishment meted out to Terry for his racist abuse was too lenient.
London's Metropolitan Police have also launched an investigation after a steward was injured in the aftermath of Manchester United's winning goal.
Scorer Javier Hernandez appeared to be pelted by objects from the crowd while footage emerged of a steward falling over advertising hoardings and onto the pitch.
Earlier this month, a number of black players refused to wear T-shirts promoting an anti-racism campaign in protest at a perceived lack of action about the problem from the game's leading bodies.
The Clattenburg case came on the same afternoon as referee Andre Marriner earned the wrath of Everton manager David Moyes, who felt that Uruguay striker Luis Suarez should have been sent off for a bad tackle in Sunday's Merseyside derby against Liverpool, which ended 2-2 at Goodison Park.
Suarez himself was at the center of a racism row earlier this year, receiving an eight-match ban after being found guilty by the FA of racially abusing Manchester United defender Patrice Evra.
Four years ago, Evra, who played against Chelsea on Sunday, was banned for four matches and fined £15,000 after clashing with a groundsman at Stamford Bridge, with the FA saying that charges that Sam Bethell used racially abusive language towards the France international could not be proven.
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The match was the longest in Premier League history due to two lengthy delays for injuries. While 12 minutes were added on, almost 13 were played -- for a total of 102 and 43 seconds that beat the previous longest in 2011 between Arsenal and Liverpool. 7, 2012 in Manchester, England.
Swansea City's Dutch goalkeeper Michel Vorm was taken from the pitch on a stretcher after suffering a groin injury when he failed to stop Tevez's long-range effort in the 61st minute.
City defender Micah Richards was later also stretchered off after suffering an apparently serious knee injury.
Manchester City manager Roberto Mancini, criticized for his tactics during the midweek Champions League defeat at Ajax, was forced to make a halftime substitution due to an injury to Aleksandar Kolarov. He brought on striker Mario Balotelli.
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