New legacy bodies will be under legal obligations to be "fair, balanced and proportionate", the Prime Minister said yesterday.
Her comments came after a former Tory minister raised concerns over the decision to re-open "so-called legacy" cases involving past and present members of the Armed Forces in Northern Ireland.
Last year, two former soldiers were told they were to be prosecuted for the 1972 murder of Official IRA commander Joe McCann.
A third case involves a retired soldier, Dennis Hutchings, who is accused of attempting to cause grievous bodily harm in relation to the fatal shooting in 1974.
A number of veterans based here during the Troubles have also received letters asking for statements about deaths.
Conservative MP Richard Benyon raised the issue during Prime Minister's Questions yesterday as he argued that soldiers who served in Northern Ireland "should feel appreciated for the difficult job they did (and not be) hounded into old age by investigations of this kind".
He said: "I know that she (Mrs May) will be as alarmed and angered as many at the decision of the Northern Ireland judicial authorities to reopen 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?"
Mrs May replied: "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.
"The overwhelming majority served with great distinction and we do indeed owe them a great debt of gratitude.
"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 .
"It will 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 and as he will appreciate, the investigations by the PSNI are of course a matter for them as they are independent of government."
Speaking afterwards, Sinn Fein MLA Linda Dillon said claims that investigations into legacy cases were disproportionate were untrue.
"British forces were directly involved in State-sponsored killings and also in a campaign of systemic collusion and State-sanctioned executions through surrogate unionist death squads," she added.
"There was nothing proportionate about their actions. There is no witch-hunt. It is due process."
At the weekend, a former head of the Army said he was certain all soldiers were properly investigated for their conduct during the Troubles.
General Lord Richard Dannatt claimed there was a witch-hunt to prosecute ageing troops.
He also maintained that it was "thoroughly unreasonable" to expect soldiers to be able to recall in detail events that happened decades ago.