The UK has announced plans for a statute of limitations which would end all prosecutions of ex-paramilitaries and former members of the security forces in legacy cases.
On Wednesday, Secretary of State Brandon Lewis told the House of Commons he plans to bring the legislation to parliament in the autumn.
The Irish premier said the proposals were “wrong for many, many reasons” and called on the UK Government to honour the Stormont House Agreement.
Mr Martin told Irish parliament: “The introduction of what amounts to a general amnesty for all security personnel, and all paramilitaries, for murders and other crimes, up until the Good Friday Agreement is not the right way to go.
“It’s wrong for many, many reasons.
“I’ve stated that consistently.
“I don’t believe in a general amnesty for those who committed murder, whether there were State actors, or whether they’re involved in terrorist or illegal organisations.
“I just don’t believe in that.
“We’ve consistently said that at the British Irish Government Council, there was an agreement to continue engagement with all parties and victims groups on these issues.
“That process has now started, as you know.
“The British Government may be setting out its position.
“But our position as an Irish Government, shared with all of the political parties in the North and all of the victim groups, remain consistent with that of Stormont House.”
The Stormont House Agreement of 2014 included provisions to investigate killings and other crimes associated with the Troubles.
These included the establishment of a Historical Inquiries Unit, an Independent Commission on Information Retrieval, an Oral History Archive and the creation of an Implementation and Reconciliation Group.
However, the British Government failed to implement the terms of the agreement and has instead moved to limit historical investigations.
The move has been slammed by victims and political parties in Northern Ireland, who criticised them as a “de facto amnesty”.
Raising the issue with the Taoiseach on Wednesday, Sinn Fein leader Mary Lou McDonald said the proposals were an “insult to victims and their families.”
She said they would create an amnesty for “British soldiers who went into the streets and gunned down innocent civilians in Derry, Ballymurphy and beyond”.
She added: “An amnesty for State and non-State actors that acted on behalf and in collusion with the British State.
“People who always believed that they would never be held to account for their actions, and that the truth behind Britain’s dirty war in Ireland would remain forever hidden by the British state.”
She continued: “This is an insult to victims and their families.
“It’s an act of absolute bad faith on the part of the British government and it’s left victims and survivors and their families believing that this is a fait accompli, a unilateral action from the British government and that the Stormont House Agreement has now been binned.”
Foreign affairs minister said the proposals set out by the British Government do not reflect what the majority of people want in Northern Ireland.
Simon Coveney said the Stormont House Agreement is the “most balanced approach” in dealing with legacy issues.
“It ensures that people can achieve justice, if there is an evidence file that allows them to do that in court,” Mr Coveney said.
“What the British Government is now saying is that they don’t believe that there should be a legal route to justice any longer for Troubles-related crimes and incidents.
“I don’t believe that reflects what the majority of people in Northern Ireland want.
“It’s certainly not what political parties in Northern Ireland are willing to support, and victims groups that have spoken to me want the option of a justice-based truth approach in court as well as the potential for a prosecution and a conviction.
“The British Government have announced their perspective on this, through a statement.
“Unfortunately that has been briefed and reported in the British media as a fait accompli, as if that is now what the British Government has decided and that is what is going to happen.
“This is a British paper contributing to that in terms of their approach in how to deal with the legacy of the past and the pain that comes with that.
“Our starting position is Stormont House, that is what was negotiated and agreed by parties in Northern Ireland.
“If there are new approaches, we will approach talks with an open mind but be firmly of the view that an amnesty through a statute of limitations is not a basis for moving forward.”
More than 3,500 people died during the Northern Ireland Troubles, which stretched from the early 1970s to the Good Friday/Belfast Agreement in 1998, while tens of thousands more were injured.