Karen Bradley is facing calls to resign after she told MPs that killings by the security forces during the Troubles "were not crimes".
The Northern Ireland secretary provoked fury when she claimed fewer than 10 per cent of deaths during the conflict were committed by the military and police, who were only "fulfilling their duties in a dignified and appropriate way".
Her comments come at a sensitive time, as the families of the Bloody Sunday victims wait to hear whether soldiers involved in the killing of civilians in Derry in 1972 would face prosecution.
In response to a question from the DUP's Emma Little-Pengelly, Ms Bradley told the Commons: "Over 90 per cent of the killings during the Troubles were at the hands of terrorists, every single one of those was a crime.
"The fewer than 10 per cent that were at the hands of the military and police were not crimes.
"They were people acting under orders and under instruction and fulfilling their duties in a dignified and appropriate way."
She later issued a clarification, saying her comments "might have been open to misinterpretation".
SDLP leader Colm Eastwood accused her of "publicly interfering with the rule of law" and called for her to step down from her post.
He tweeted: "No-one has the right to deliberately pressure or intervene with due process. She should resign."
John Finucane, whose father Pat was murdered by loyalist paramilitaries possibly colluding with British security forces, said: "Legally, politically and morally these comments are indefensible, yet is it really surprising to hear a SoS [secretary of state] publicly express the contempt we know the British government had for lives here?"
Michelle O'Neill, Sinn Feinn vice president, said: "British politicians cannot be allowed to ride roughshod over the legal system.
"No one can be above the law and bereaved families, some of whom have been campaigning for almost five decades, are entitled to access to truth and justice.
"These offensive and hurtful comments should be withdrawn immediately."
The DUP's Sir Jeffrey Donaldson said it was vital for the government to support veterans, but added: "However no one should be above the law and all innocent victims deserve justice."
Ms Bradley later clarified her comments in the Commons, saying: "The point I was seeking to convey was that the overwhelming majority of those who served carried out their duties with courage, professionalism, and integrity and within the law.
"I was not referring to any specific cases but expressing a general view. Of course, where there is evidence of wrongdoing it should always be investigated whoever is responsible.
"These are of course matters for the police and prosecuting authorities who are independent of government."
The Public Prosecution Service in Northern Ireland is expected to announce its decision next week on whether former paratroopers involved in the Bloody Sunday shootings would be prosecuted.
Theresa May told MPs that the current system for investigating the legacy of the Troubles "needs to change" to provide better outcomes for both victims and survivors, and confirmed the government was looking at potential legislation to ensure soldiers are not "unfairly pursued through the courts".
Ms Bradley, who is a close ally of Ms May, previously faced criticism when she admitted that she did not realise nationalists in Northern Ireland did not vote for unionist parties in elections.
She said she did not understand campaigns were generally fought within each part of the community - rather than across it - at the time of her appointment.
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies