A government proposal to end all Troubles prosecutions has been widely criticised.
It would apply to military veterans as well as ex-paramilitaries.
The proposals, described by Prime Minister Boris Johnson as allowing Northern Ireland to “draw a line under the Troubles”, would also end all legacy inquests and civil actions related to the conflict.
They also include a new truth recovery body and an oral history initiative.
Government is set to consult with political parties and victim groups before introducing legislation in the autumn.
Mr Lewis told the Commons: “We know that the prospect of the end of criminal prosecutions will be difficult for some to accept and this is not a position we take lightly.
“But we’ve come to the view that this is the best and only way to facilitate an effective information retrieval and provision process, and the best way to help Northern Ireland move further along the road to reconciliation.
“It is in reality a painful recognition of the very reality of where we are.”
Political parties and bereaved families have criticised the statute of limitations as a “de facto amnesty”.
Irish prime minister Micheal Martin said the proposals were “wrong for many, many reasons”.
DUP leader Sir Jeffrey Donaldson said the statute of limitation “would be rejected by everyone in Northern Ireland who stands for justice and the rule of law”.
Northern Ireland’s deputy First Minister Michelle O’Neill accused the UK of introducing an amnesty “to protect state forces from their ‘dirty role’ in Ireland”.
The relatives of one of the 10 killed by soldiers in the Ballymurphy area of west Belfast in 1971 have vowed to mount a legal challenge to the proposals.
Eileen McKeown, daughter of Joseph Corr, said the proposals “will not be tolerated and will be legally challenged”.
“The Ballymurphy Massacre inquest findings show how the law should work independently,” she said.
“All victims need to know the truth, they need to know what happened to their loved ones.
“We all bleed the same blood so everybody needs truth and justice and then maybe they can start living their lives.
“We spent 50 years trying to prove that our loved ones were innocent, there are loads of families out there like us and they all need to know the same thing.”
Speaking earlier during Prime Minister’s Questions, Boris Johnson said: “The people of Northern Ireland must, if we possibly can allow them to, move forwards now.
The Prime Minister added: “The sad fact remains that there are many members of the armed services who continue to face the threat of vexatious prosecutions well into their 70s, 80s and later, and we’re finally bringing forward a solution to this problem, to enable the province of Northern Ireland to draw a line under the Troubles, to enable the people of Northern Ireland to move forward.
“I think someone with greater statesmanship and clarity of vision would have seen that and given these proposals a fair wind.”
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.