The IRA's decision to withdraw its offer to put guns beyond use could play into the hands of sceptics who always doubted its intentions, the Northern Secretary said.
Dr John Reid said there would be a great deal of scepticism about any claim that the one-day suspension of the institutions at the weekend warranted the IRA's response.
"Withdrawing from an agreement which took two years to arrive at, only five days after republicans declared it as historic, can only play into the hands of those sceptics who have always doubted their intentions.
"If in five or six days they can decide that a one-day suspension of an Assembly that wasn't sitting, on a Saturday, during the holidays, in August, was sufficient grounds for taking such an historic step backwards, then I think there will be a great degree of scepticism," he said.
Dr Reid's comments came amid allegations that three men arrested in Colombia were IRA members. The Northern Secretary said the IRA arms announcement would, together with reports from Colombia, disappoint many people.
"I think we had made a historic, or at least a significant, move on decommissioning last week, and it has taken so long to get there with such effort and proclaimed to have been of such a significant nature by republicans themselves, that to have broken that agreement and walked away from it within a week will not be easily understood home or abroad," Dr Reid said.
He understood the difficulties facing republicans but added: "This announcement does not fundamentally change the process. We will continue to work towards the full implementation of the agreement."
The British government would continue to try to implement the proposed reforms of policing and criminal justice.
"If others want to walk away from this process, it's up to them. They will make their own judgment. They will take their own counsel and they will have to give their own explanations to people," he added.
"We have always acted in good faith, and we will continue to act in good faith. We are not the ones who are walking backwards on this, nor will we be, and I will continue with those elements.
"Decommissioning remains an indispensable part of that agreement, and I will not be deflected from proceeding with those parts of the agreement, like creating a new police service and the renewal of the criminal justice system, which are of benefit to all the people," Dr Reid said.