SINN Fein TD Dessie Ellis is under growing pressure to make a Dail statement on secret state documents that suggest he was involved in as many as 50 murders during the Troubles.
Mr Ellis is rejecting the allegations, but is facing calls to make a full statement to explain his IRA past.
British state papers from 1982, released under the 30-year rule, reveal Mr Ellis is believed to have been involved in the murders in the Republic and Northern Ireland.
Fianna Fail justice spokesman Niall Collins said Mr Ellis must make a Dail statement and outline the "true facts of his involvement in these activities over the years".
Mr Collins said: "Dessie Ellis should make a personal statement to the Dail after the Christmas break.
"He should outline all the facts of his involvement in these activities. An elected deputy to Dail Eireann cannot keep secrets crucial to their past concealed."
The internal communications within the British government suggest that Mr Ellis, then a member of the IRA, was forensically linked to the deaths.
And another communication dealing with Mr Ellis, now a TD for Dublin North-West, refers to him as a "leading PIRA" (Provisional IRA) member.
He admits to being involved in the "highest levels" of the IRA.
Mr Ellis was sentenced to 10 years in prison on explosives charges in the 1980s and he was the first person charged under the 1987 Extradition Act for an explosives charge in England.
He then went on a hunger strike that lasted 37 days in protest against his pending extradition to England. He was eventually acquitted in London.
Mr Ellis was elected a TD in 2011 on his third attempt but declined to comment yesterday.
But Mr Flanagan said that "these matters can no longer be treated by Sinn Fein in a routine way. "Deputy Adams has suggested the establishment of an Independent Truth Commission as a means of resolving our past conflict," he added.
"If this is to be the case, let Dessie Ellis be the first person to be brought before it, so that questions can be answered in respect of the 50 people murdered, to which the British government suggests he is in some way linked," he said.
Mr Ellis in a statement later described the British claims as "unsubstantiated" and from the same "shadowy forces who murdered so many Irish citizens over the years".
"I'm sure that it hasn't escaped Deputy Flanagan's attention that I was cleared by a British court of these trumped-up allegations, which begs the question as to where he is coming from," Mr Ellis added.
"Mr Flanagan mentions without any hint of irony the need for an independent truth and reconciliation commission despite the fact that it is Sinn Fein who have led such calls and despite the fact that Mr Flanagan's Government has done nothing at all to support the establishment of such a process.
"Let me say that I am very proud of my involvement in the republican struggle over the years and of the leadership role republicans have played in the peace process, despite the best efforts of nay-sayers such as Charlie Flanagan and his ilk," he added.
Mr Ellis had earlier declined to comment when approached by the Irish Independent.
When asked if he thought that any of the bombs he made resulted in any deaths, he replied: "Honestly, I'm not going to comment on anything."
Mr Flanagan said that this approach was not good enough.