Prime Minister David Cameron was "rash" to rule out any further Bloody Sunday-style inquiries, former NI Secretary Shaun Woodward has said.
MPs have been debating the tribunal's final report published in June after 12 years at a cost of about £200m.
Mr Woodward warned that Mr Cameron's pledge for "no more open-ended and costly inquiries into the past" could be exploited by dissident republicans.
NI Secretary Owen Paterson said it was not just a "financial calculation".
"To continually pick out selective cases for lengthy public inquiry is not a viable approach to dealing with the legacy of a conflict that saw thousands of people from all parts of the community killed," he said.
"Helping families and wider society achieve greater understanding and closure is vital, however difficult that may be.
"I plan to continue exploring ideas on the contentious issues of the past over the coming months. Our approach will remain measured, sensitive and realistic."
Relatives of those killed on Bloody Sunday were in Westminster to watch the debate on the findings of the Saville Inquiry.
Mr Paterson again apologised on behalf of the government for Bloody Sunday, in which Parachute Regiment soldiers opened fire during a civil rights march in Londonderry killing 13 people on 30 January 1972.
He said the processes involved with understanding events from the Troubles were now "in the hands of the devolved administration".
Mr Paterson said the Historical Enquiries Team (HET), which is investigating unsolved murders from during the Troubles, had achieved an "86% satisfaction rate", something which he said "demonstrates the success it's having in helping to bring a measure of resolution".
Mr Woodward warned ministers that dissidents in Northern Ireland would be "watching very carefully how the British government now responds to the Saville Report".
"They wish to see how the grief of others can be exploited, how justice can be turned to injustice," he said.
"They wish to pervert the outcome, to twist the truth in perverted logic which can be used to build community support for a violent struggle in the years ahead."
Another former Northern Ireland Secretary, Labour MP Paul Murphy, said he had no regrets about setting up the inquiry.
"That was the right thing to do: right in the first instance because we wanted to see that justice was done and the truth came out, and secondly, of course, because it was part of the wider political picture in dealing with the peace process at that time and since then.
"I haven't the slightest doubt in my mind that had we not tackled the issue of Bloody Sunday in the way that we did, there would not have been a successful peace process."
DUP MP Gregory Campbell said the inquiry did not take proper account of the situation in Northern Ireland at the time, when "murder, mayhem and terror were rife".
Mr Campbell said Sinn Fein Deputy First Minister Martin McGuinness had failed to co-operate fully with the inquiry.
"Unfortunately he refused to go into any detail about his involvement in the IRA on that day," he said.
"Lord Saville concluded that he 'probably' had in his possession a machine gun on that day."
He added: "It would appear that there are some people who are demanding prosecutions of some soldiers who complied with the Saville Inquiry, who answered all the questions that were posed to them throughout the Saville Inquiry.
"But there does not appear to be the same eagerness or intensity of purpose of saying that we should also look at the prosecution of someone who probably had a machine gun on that day."
SDLP leader Margaret Ritchie said there should be an inquiry into the killings of 11 people in the Ballymurphy area of west Belfast in August 1971.
A Catholic priest and a mother of eight were among the 11 shot dead during a three-day operation that was designed to round up suspected republican paramilitaries.
"Those families lost loved ones, and the connection is that they were all shot by members of the Parachute Regiment," she said.
"It is also believed - and I put it like that - that some of those soldiers could have been involved in Bloody Sunday on the streets in Derry.
"Those families in Ballymurphy need truth. Ways have to be found to relieve their immeasurable grief. They require redress and compassion from the state. They require that stigma to be removed from them and for the innocence of those people who were killed to be declared."
Meanwhile, a US human rights group has described the report's findings as courageous yet flawed.
The International League for Human Rights said that there should have been greater focus on the behaviour of senior military officials.
The inquiry was the longest running in British legal history and cost about £200m between 1998 and 2010.
The report was heavily critical of the Army and found that soldiers fired the first shot.
It concluded that none of the casualties was posing a threat or doing anything that would justify their shooting.