Patrice Evra was fuming after the 1-1 draw, claiming in an interview with Canal Plus that Luis Suarez had racially abused him on a number of occasions during the game.
Although the full-back feels TV replays will prove his claims, Suarez has denied them strongly, and has been backed by Liverpool.
Evra is adamant though and United have vowed to support their man, even though Ferguson accepts it places them in a tricky situation.
"It is not an easy one for us," said the United boss.
"It is not something we would want to level against Liverpool and it is not against Liverpool
"Obviously Patrice feels very aggrieved at what was said to him.
"I have spoken to him and he is adamant he wants to follow it on so it rests in the hands of the FA now."
Evra is expected to start Tuesday's Champions League encounter with Romanian champions Otelul Galati in Bucharest.
However, it seems just a matter of time before United register an official complaint with the FA that will have to be followed up by interviews with representatives of both clubs.
"Everyone knows Manchester United and Liverpool have great responsibilities in terms of things that happen on the field.
"Saturday was terrific. Both sets of fans were good. There was not any of that silly chanting we have had in previous years. Both sets of fans deserve praise for that."
UEFA and FIFA repeatedly stress their anti-racism stance, yet have fined countries paltry sums when players of international teams have been the subject of racist taunts.
Earlier this month UEFA warned Bulgaria they face a disciplinary hearing into racist taunts during their Euro 2012 qualifier with England in Sofia earlier in the season, although that has been put back to November 17.
"I am not aware of any instances in terms of British football," admitted Ferguson.
"We concentrate on our own game. What happens in other countries I am not really sure.
"It doesn't happen in England. There are very few examples of that.
"Since I have come down we have had some fantastic players at Manchester United who have been black.
"It is not an issue for the game itself. Maybe this is what surprised Patrice Evra. He thought he was slighted on Saturday.
"We don't want to see it. It is as simple as that."