On Thursday, the 30-year-old was fined £2,000 after pleading guilty to assault and resisting arrest following an incident outside a nightclub in Jersey.
"We have high standards that we expect across the game, in line with rugby's core values, from all those involved within it," RFU head of discipline David Barnes told reporters.
"I have this afternoon taken the decision to charge Danny Cipriani."
Gloucester chief executive Stephen Vaughan has subsequently criticised the timing of the RFU charge.
"We are surprised and extremely disappointed to have recently received notification of disciplinary action," Vaughan said in a statement.
"We do not agree with the RFU's decision to embark upon a disciplinary process before we have concluded our own internal discussions."
Cipriani's disciplinary hearing will take place next week, while the date, time and members of the independent RFU panel have yet to be confirmed.