Theresa May has faced concerted pressure from Conservative backbenchers at prime minister’s questions over what they said was the unfair targeting of military veterans over incidents that took place in Northern Ireland many years ago.

Iain Duncan Smith, Owen Paterson, Mark Francois and Johnny Mercer insisted that the veterans did not seek a blanket amnesty, but believed they were being targeted for prosecution when those who carried out terrorist attacks were not.

May insisted this was not the case, saying the government was seeking to come up with a fair system for delayed prosecutions which did not risk covering both veterans and former terrorists with a blanket amnesty.

In sometimes angry scenes, the prime minister faced shouts from some MPs as she sought to defend the government over a hugely contentious issue that has angered many Tories, and has seen the new defence secretary, Penny Mordaunt, suggest the idea of an amnesty for Northern Ireland veterans.

At the weekend, reports claimed Downing Street was blocking changes that could protect veterans from prosecution.

Duncan Smith, addressing the question first, referred to his service in Northern Ireland, and the murder of a friend there, saying: “I must say that none of those who served have called for an amnesty. What they have called for is fairness and justice.”

Referring to new investigations of cases veterans believed closed, he said: “How can I say to my old colleagues that this government has not abandoned them?”

In response, May said the current system had “a disproportionate emphasis in terms of cases that involve the police and the armed forces”, which a new approach would seek to end.

Following up, Paterson said the PM had not answered the question, saying veterans sought “a categoric assurance that the prosecuting authorities within the existing framework of law will not bring forward a fresh process unless there is categorical, clear new evidence, and there is an assurance and no doubt whatever that a fair trial will proceed”.

May repeated her point that existing systems on the issue “have been found to be flawed”.

She said: “That is why it is necessary to go through the work we have been doing to find a process that will not be flawed, that will be legally supportable and will enable the fairness and justice that we all want to see to be brought to the fore.”

In a more emotional intervention, Francois read a question from a former marine, David Griffin, under investigation for the fatal shooting of an IRA member in 1972.

In the letter, Griffin said the government was “pandering to Sinn Féin/IRA, while throwing veterans like me to the wolves”.

May rejected the argument, saying: “I don’t want to see a system where there is an amnesty for terrorists. I want to see a system where investigations can take place in a lawful manner, where the results of those investigations can be upheld and will not be reopened in the future, and in order to do that we need to change the current system. And that is what we will do.”

Mercer began by saying May should be “beginning to understand the level of fury of veterans in this country”. There was, he said, a “disturbing” insinuation that veterans and terrorists would be treated with equivalence, adding: “The line that preferential treatment should not be given to veterans is not right.”

May said she had repeatedly stressed that she valued the service of veterans, adding: “There is no question of equating that bravery and that sacrifice with the acts of terrorists.”

But to impose a blanket amnesty, she said, would do this. “Any statute of limitations, any amnesty that is put into place would, as a matter of law, have to apply across the board. I do not want to see, and I will not see, an amnesty for the terrorists.”