About 30 protestors, including those related to the 21 victims of the Birmingham pub bombings, picketed the conference, held in the London Irish Centre in Camden.
They carried banners which read 'Justice For The 21' and 'Gerry and The Peacemakers Will Always Walk Alone While IRA Victims Are Ignored'.
A group of the protestors carrying a loyalist flag also confronted Sinn Féin members and others leaving the Irish centre and accused them of attending a "murderers' covenant".
Police also had to intervene to stop family members of those killed by IRA bombs from clashing.
Campaigners for those killed in the Birmingham pub bombings accused Colin Parry, whose son died in an IRA blast in Warrington, of "rubbing shoulders" with those responsible for the attacks.
The confrontation came after Mr Parry delivered a speech at the conference about the work of the peace foundation he established to honour his son and a three-year-old who was killed by the same blast.
It hurts that somebody would be so unaware of what we do that they could accuse me of kowtowing to terrorists.
Mr Parry said he was hurt by the accusations that he was an "IRA apologist".
He said: "We can all yell and scream at each other over barricades, but that won't get us anywhere."
Brian Hambleton, whose 18-year-old sister Maxine was killed in the 1974 Birmingham attacks, said: "He wants us all to jump on the Jolly Roger with him and Gerry Adams.
"I told him that I am fighting for his son as well as my sister.
"How he can have a drink and a sandwich with that man is beyond all human recognition."
Mr Hambleton appealed to Mr Adams to speak with him and other relatives of the Birmingham victims, but claimed: "They will only talk to people that tell them what they want to hear."
They are talking about a new phase of the peace process but are not willing to face up to what they did and address the suffering of the members of our community.
Also speaking at the 'Towards a New Ireland' conference, were a host of people from various political, community and business backgrounds.
Jonathan Powell, former chief of staff to Prime Minister Tony Blair during the time of the Good Friday Negotiations and local MLA John McAllister from NI21 delivered speeches during the event.
During his speech Gerry Adams said he "understood" the grief of relatives of the Birmingham and Warrington killings.
He said: "As a republican leader I have never and I will never distance myself from the actions of republicans.
"I've shouldered too many problems, been to too many gravesites."
I understand the scale of the loss and the grief that exists in our communities - families in Birmingham, Guildford and Warrington.
The Sinn Féin president hailed Mr Parry, who last month invited Deputy First Minister Martin McGuinness to speak at the commemoration of the 15th anniversary of the Warrington bombing, as an "inspiration".
Tim Parry and three-year-old Johnathan Ball were killed when bombs, planted in litter bins in Warrington's main shopping area, exploded in 1993.
No warning was given and, as well as the fatalities, the blast injured 56 people.
Six men were convicted and served 16 years in prison over the bombings in Birmingham's Tavern in the Town and Mulberry Bush pubs in November 1974.
Their convictions were quashed by the Court of Appeal in 1991 and no one has been brought to justice since.