Official state documents released by the British government state that there is forensic evidence linking Ellis to killings on both sides of the border.
The news prompted Fine Gael chairman Charlie Flanagan to call for Ellis to be brought in front of an independent Truth Commission to be grilled over past activities.
But the Sinn Fein politician last night said that the claims were "created by the Brits" and rejected any suggestion that he should resign his seat.
"This is old wood being rehashed. I reject any calls that may come for my resignation. This was stuff used against me when I was in America facing extradition. It's proven upsetting for my family, to be honest," he said.
Asked to comment on the "50 murders" he is alleged to have been involved in, Deputy Ellis replied: "I don't know where they are getting these figures from so I'm not going to comment on that, I haven't even read the papers to be honest."
But speaking to the Herald, the Dublin North West TD cryptically admitted that he was forced into situations he "regrets" during his involvement with the IRA.
"I've been a republican all my life and I don't try and hide that. People across all movements, republican and loyalist, have been forced into situations that they regret and I'm no different," he told the Herald.
He then launched a ferocious attack on Fine Gael chairman Charlie Flanagan.
"The likes of [Charlie] Flanagan and others can latch on to this all they like. But they should be careful about what they say about people.
"I've been in politics long enough to know that there are a lot of people out there who don't want people like me, or Sinn Fein, doing well. They'll use it against me in the Dail but I'll be ready for that."
Deputy Flanagan told the Herald that he would not be "intimidated" by Deputy Ellis or "anybody in Sinn Fein", adding that the claims must be brought to light in front of an independent commission.
"We cannot simply forget the past and sweep the issues which strike at the very heart of the democratic process under the carpet to suit Sinn Fein.
"Deputy Adams has suggested the establishment of an Independent Truth Commission as a means of resolving our past conflict.
"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."
The document mentioning Deputy Ellis is among papers from the 1980s which were released this week under the '30-year rule'.
It was sent from the British embassy in Washington to officials in London.
In a statement to the Herald, a Sinn Fein spokesman described the claims as "unsubstantiated allegations".
"Irish Republicans do not attach any value to claims made in secret documents emanating from the British secret services, who were responsible for countless murders in Ireland during the course of the conflict."