New legacy bodies will be under legal obligations to be "fair, balanced and proportionate" the Prime Minister has said.
The comments come after a Tory former minister raised concerns over the decision of the Northern Ireland judicial authorities to re-open "so called legacy" cases involving past and present members of the Armed Forces.
Conservative Richard Benyon, MP for Newbury, raised the issue during Prime Minister's Questions as he argued those who served in Northern Ireland "should feel appreciated for the difficult job they did not being hounded into old age by investigations of this kind".
He said: "I know that she will be as alarmed and angered as many at the decision of the Northern Ireland judicial authorities to re-open the so called legacy cases involving past and present members of the Armed Forces.
"These cases are being meticulously investigated and represent just 10% of deaths in the Troubles.
"A line really does need to be drawn here. Does she agree that it is wrong to single out any group for this kind of investigation and that the hundreds of thousands of people who served in Northern Ireland should feel appreciated for the difficult job they did not being hounded into old age by investigations of this kind."
Theresa May replied that "we are unstinting in our admiration for the role that our Armed Forces played in ensuring that Northern Ireland's future would only ever be decided by democracy and consent".
She added: "And the overwhelming majority served with great distinction and we do indeed owe them a great debt of gratitude.
"But as part of our work to implement the Stormont House Agreement we will ensure that new legacy bodies will be under legal obligations to be fair, balanced and proportionate.
"That will make sure that our veterans are not unfairly treated or disproportionately investigated and will indeed reflect the fact that 90% of deaths in the Troubles were caused by terrorists and not by the Armed Forces.
"But of course as he will understand, as he will appreciate, the investigations by PSNI (Police Service of Northern Ireland) are of course a matter for them as they are independent of Government."