Catholic Bishops have written to Secretary of State Brandon Lewis expressing their "deep concern" at the Government's proposed approach to dealing with legacy issues.
Last month the Government said ending the cycle of re-investigations when there is no new compelling evidence would deliver on its promise to protect former members of the armed forces from "vexatious claims".
Under the new proposals, once cases have been considered, there will be a legal bar on any future investigation.
But Catholic Church leaders, led by Archbishop of Armagh Eamon Martin, said there was "alarm and disappointment at the new position which the Government is taking to address the legacy of the past in Northern Ireland".
They referred specifically to what they described as the Government's "departure from the understanding inherent in the Stormont House Agreement to which all parties signed up with goodwill".
"It is deeply concerning that the Government has departed from this fundamental principle and has moved away from the position of equal access to justice for all," the letter said.
"We must consider the actions of all. State and non-state actors must be equally accountable before the law. Otherwise, no authentic reconciliation can be achieved. We therefore support the ongoing pursuit of appropriate criminal, legal and civic justice for all victims.
"The timing of the announcement was unfortunate, when we are dealing with the coronavirus pandemic.
"The implications of the proposals are therefore not receiving the scrutiny they might otherwise receive.
"We also caution that any specific provisions for Northern Ireland could destabilise the Executive and other institutions and would undoubtedly provoke significant political and public reaction at a time when a strong and unified Executive is needed more than ever."