The Italian was sent to the stands from the touchline by referee Neil Swarbrick in the 43rd minute of Chelsea's 1-0 win at Stamford Bridge on Wednesday after protesting about the award of a Swansea goal kick.
Conte, who watched the second half on a screen in the dressing-room, apologised for his behaviour.
“I was frustrated for this situation," he said. "I tried to tell again, but then the referee took this decision. I repeat, I apologise for this. For sure I made a mistake.”
He has until 6 PM GMT on Tuesday to respond to the charge.
(Reporting by Christian Radnedge, editing by Ed Osmond)
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