The BBC has apologised after a floor plan for the BBC Question Time programme referred to John O'Dowd as 'Sinn Fein/IRA'.
The clip board attached to a camera in the studio detailed the position of the panellists.
The show was broadcast from Belfast on Thursday evening.
The BBC said the note was written by one of the technical staff for his own use.
Earlier, Sinn Fein said they were seeking an immediate explanation for the note, which the BBC has described as "insensitive and extremely naïve".
Mr O'Dowd said he had agreed to take part in the programme on the basis of "respect and equality".
"After the programme was finished I was made aware of the floor plan pinned to a camera branding me a member of 'SF/IRA'. This was not on the floor plan previously shown to me before filming," he said.
Mr O'Dowd, who is Northern Ireland's minister for education, described it as "serious issue".
"The 'SF/IRA' tag was one created at the height of the unionist murder campaign against my party colleagues in the late 1980s and early 1990s. It was an attempt to justify attacks on Sinn Fein members and our families," he said.
"For the BBC to adopt the tag 20 years into a peace process is beyond belief."
Ulster Unionist justice spokesperson Tom Elliott called Mr O'Dowd's comments "utterly laughable".
"First we had Gerry Adams claim he was never a member of the IRA. Then we had Martin McGuinness tell us that he was a member - indeed a commander in Londonderry - but left in 1974.
"Now John O'Dowd has lodged a formal complaint and asked for an explanation as to why a BBC Floor plan was altered to read Sinn Fein/IRA.
"For a Sinn Fein representative to ask why that party would be linked to the IRA is utterly laughable.
"If this is evidence of Sinn Fein wishing to distance itself from the murderous activities of the IRA then that is of course to be welcomed.
"The trail of death and destruction wreaked across Northern Ireland, into the UK mainland the Republic of Ireland and even further afield is something which any right thinking person or political party should be ashamed of."
The picture was taken and tweeted By Simon Whittaker, who was a member of the audience.
"My issue is that it is more about impartiality - we were told this is your show, we're asking the questions you want to be answered and the key is it's impartial," Mr Whittaker said.
"This is 2013, yet the DUP are advertised as the goodies and Sinn Fein the IRA.
"I'm sure it wasn't done maliciously and maybe it was by people who don't understand the context of Northern Ireland.
"But it wasn't what you would expect to see."
Mr O'Dowd said: "We lodged a formal complaint with the BBC in Belfast seeking an immediate explanation for the sign and what action is to be taken against those behind it.
"We await with interest their response. But one thing is for sure we will not let the BBC simply sweep this issue under the carpet."
In a statement the BBC said: "The BBC is very sorry for any offence caused. The note was written by one of the technical staff on the programme for his own use.
"It was not authorised or endorsed by anyone on Question Time. The person responsible has been left in no doubt that it was inappropriate, insensitive and extremely naïve.
"We are sure viewers of last night's programme will be clear that this note had absolutely no bearing on the content of the show."
Question Time is produced by independent company, Mentorn Media for the BBC.