Karen Bradley has apologised for her remarks suggesting security force killing were "not crimes" but people acting "under orders and under instruction and fulfilling their duties in a dignified and appropriate way".
The Secretary of State has faced a barrage of criticism with growing calls for her to resign. She later "clarified" her remarks saying they were "open to interpretation".
She refused to apologise on Wednesday night.
In a statement just before noon on Thursday, a statement was released by the Northern Ireland office.
The Secretary of State said: "Yesterday I made comments regarding the actions of soldiers during the Troubles.
"I want to apologise. I am profoundly sorry for the offence and hurt that my words have caused. The language was wrong and even though this was not my intention, it was deeply insensitive to many of those who lost loved ones."
She continued: "I know from those families that I have met personally just how raw their pain is and I completely understand why they want to see justice properly delivered.
"I share that aim and that is why I launched the public consultation on addressing the legacy of the troubles.
"My position and the position of this Government is clear. We believe fundamentally in the rule of law. Where there is any evidence of wrongdoing this should be pursued without fear or favour whoever the perpetrators might be. That is a principle that underpins our approach to dealing with legacy issues and it is one from which we will not depart."