The current investigation into soldiers and police who served in Northern Ireland during the Troubles is "patently unfair", according to Theresa May.
The Prime Minister's comments came as senior Tories hit out at proposals which could see British soldiers prosecuted for offences during the conflict.
While most of those killed and injured during 30 years of violence were at the hands of paramilitaries, members of the security forces were responsible for a significant number.
Mrs May said, "the situation we have at the moment is that the only people being investigated for these issues that happened in the past are those in our Armed Forces or those who served in law enforcement in Northern Ireland - that is patently unfair.
"Terrorists are not being investigated, terrorists should be investigated and that is what the Government wants to see."
The comments came after Julian Lewis MP asked if the Prime Minister would ensure a statute of limitations would not be excluded from the upcoming consultation.
This would prevent anyone from facing trial for offences that happened during the conflict, including former servicemen and paramilitaries.
Earlier in the day, Sir Mike Penning - a former Northern Ireland and defence minister - told ministers that the consultation should "protect the soldiers and put them first, and the terrorists second."
The Secretary of State for Northern Ireland Karen Bradley also told the House that there was a "disproportionate emphasis on the actions of the military and law enforcement during the Troubles and really very little emphasis on the actions of paramilitary terrorists."
Mechanisms to deal with the conflict legacy were agreed by Northern Ireland politicians in the 2014 Stormont House Agreement; an amnesty was not among them.
The agreed proposals, including a new independent investigatory unit, a truth recovery body and an oral archive, are on ice due to a small number of outstanding disputes.