The Celtic player has been served with a second and more serious Notice of Complaint into his behaviour at a pub in Edinburgh before the Hearts v Hibs game a week past on Sunday.
The second charge states the striker was "singing in public a song of an offensive, racist and/or discriminatory nature".
This allegation relates to a song being sung about former Hearts player, Rudi Skacel.
The initial charge, based on the video footage originally released on to the web of the player among a group of Hibs fans in the Roseburn Bar, accused the 23-year-old former-Hibs loan player of not acting in the best interests of football by "singing about Hearts in administration".
Griffiths said: "It was football banter. I apologise if any offence was caused."
However, when further footage appeared over the weekend, SFA Compliance Officer, Vincent Lunny, re-investigated. At the same time, Police Scotland confirmed they had opened their own inquiry into the allegations.
When the SFA issued Griffiths with his first Notice of Complaint, the hearing was set for April 24. The second charge will also be heard then, even if the police investigation has not been concluded.
Though any decision made by the hearing at Hampden may be considered to impact on the separate police investigation, the SFA have received confirmation that, on advice from the Crown Office, they are free to proceed.
Celtic have already fined Griffiths a month's wages for his part in the singing of the song about Hearts' financial situation, but vowed to defend the player when he appeared in front of the SFA hearing.
Now, they have announced they are taking the second allegation "extremely seriously" and have launched a further investigation. Celtic are not expected to make further comment until this has been completed, and players put before the Press earlier this week were not allowed to take questions on the matter.
If found guilty by the SFA, Griffiths faces a lengthy ban which would bring his debut season at the club he joined in January to a premature end.
Celtic have only five more games to go, and four of them come after the hearing. It is another headache for manager Neil Lennon, who warned Griffiths after fining him for the first offence he had used up his one strike.
Lennon is on record as adopting a zero-tolerance stance with regard to any form of racism, and the club are being closely scrutinised over how they deal with this incident.
With no game scheduled for this weekend, Lennon has taken the opportunity to embark on a scouting mission for new players in England. And the Hoops boss is also due to sit down with some of the game's biggest hitters.
He said: "I will take in a few games and I'm going to the League Managers' Forum on Sunday and Monday. I'm looking forward to that, and to catching up with some great managers and just listening to what they have to say."