The prime minister has been accused of granting an amnesty to terrorists by one of her own MPs.
Backbencher Mark Francois was one of five Tory MPs to use PMQs to raise the issue of soldiers who had served in Northern Ireland.
He cited Army veteran David Griffin as saying former soldiers were being “thrown to the wolves”.
Mr Griffin, an ex-Royal Marine, said he shot dead an IRA man in Belfast in 1972 to stop him attacking another soldier.
“Forty seven years later, he is now being investigated by the Police Service of Northern Ireland,” said Mr Francois.
He asked Theresa May why, in Mr Griffin’s words, she was “pandering to Sinn Féin/IRA while throwing veterans… to the wolves”.
Analysis: Julian O’Neill, BBC News NI home affairs correspondent
Anger over the treatment of Northern Ireland veterans has been building and hit new heights during Prime Minister’s questions.
Current Ministry of Defence thinking is to give new protections against prosecution to those who served abroad.
If that is the scope of any legislative proposal, backbenchers will almost certainly amend it to cover the Troubles as well.
The real danger is that all this scuttles attempts to deal with the past in Northern Ireland and poisons talks to restore power-sharing at Stormont.
The Northern Ireland Office is very alive to the risks.
But is Westminster listening?
“The IRA have letters of comfort. We don’t,” Mr Griffin was reported to have said, referring to a 1999 scheme under which letters were issued to paramilitary suspects saying they were not wanted by police.
In response, Mrs May said terrorists did not have an amnesty, adding that evidence of criminal activity would be investigated.
“What I want to ensure is that we have a fair and just system,” said the prime minister, to heckles from Mr Francois, who is vice-chairman of the pro-Brexit European Research Group (ERG).
Mrs May said she did not believe the system was currently operating fairly “at the moment”, and reiterated her desire to change the system regarding cases related to the legacy of the Troubles in Northern Ireland.
Mr Francois was one of five Conservative backbenchers who raised the prosecution of Northern Ireland veterans during PMQs.
Tory MP Johnny Mercer, who has withdrawn his support for the government over the issue, said Mrs May was beginning to understand the “level of fury” over Northern Ireland veterans being prosecuted.
Mrs May reiterated that she would “not have an amnesty” that would also cover “terrorists”, and that what some of her own backbenchers wanted her to do would create an equivalence between terrorists and soldiers.
The response prompted Mr Mercer to put his head in his hands.
The embattled prime minister has been trying to persuade MPs to support her new Brexit plan, which has led to growing pressure from Tory MPs for her to resign.
Mrs May has pledged to set a timetable for a new leader to take over after MPs vote on her compromise Brexit plan in the week beginning 3 June.
However, some MPs are again seeking to change party rules, so they can vote to oust her at a meeting of backbench MPs later.
Six former soldiers who served in Northern Ireland during the Troubles are facing prosecution.
The cases relate to the killings of two people on Bloody Sunday in Londonderry in January 1972; as well as the deaths in separate incidents of Daniel Hegarty, John Pat Cunningham; Joe McCann and Aidan McAnespie.
Not all of the charges are for murder.
The Public Prosecution Service in Northern Ireland has said that of 26 so-called Troubles legacy cases it has taken decisions on since 2011, 13 related to republicans, eight to loyalists, and five are connected to the Army.