Education Secretary John Swinney has met survivors of child abuse after some groups said they had lost confidence in the government's inquiry.
Mr Swinney rejected claims that the government interfered with the inquiry in "the strongest possible terms".
He said he was determined to build on the good work of the inquiry.
Speaking after the meeting with Mr Swinney, one of the abuse survivors, Dave Whelan, said the delays to the inquiry were "upsetting".
"I am emotional about it because we've been doing this for too long," he told BBC Scotland.
"I represent a group of former Quarriers residents where eight people have been convicted. My own abuser was convicted and we're still seeking justice.
"Many, many more people where actually abused in these care homes and in these institutions."
Andrew Lavery, from White Flowers Alba, said people needed to be held to account by the inquiry.
"There needs to be not just recommendations, but societal change," he said.
"[The inquiry must] seek to repair and redress the harm of the past instead of ignoring thousands of people who were abused, which is completely wrong."
Mr Swinney told the BBC he wanted to make sure the inquiry was "entirely independent" from government.
He said: "As we work to overcome the obstacles that we have experienced in the last couple of weeks, there is good work that is being undertaken by the inquiry.
"I'm determined to build on that, to reflect on the views of survivors and to make sure that their thinking and their approach is built in to how we take forward the inquiry."
The inquiry was announced in December 2014, to investigate historical abuse of children in care at institutions, boarding schools, hospitals and in foster care.
It was formally set up in October 2015, with Susan O'Brien QC chairing, alongside psychology professor Michael Lamb and Glenn Houston.
However, Mr Lamb resigned in June 2016, saying the inquiry was "doomed" by government interference.
Ms O'Brien followed one week later, making similar claims, but with Mr Swinney announcing that moves were underway which could have seen her removed over "unacceptable" comments.
Mr Swinney called the meeting to explain to survivors why he took the decision to investigate these comments, which led to Ms O'Brien's resignation.
A child abuse expert had complained that Ms O'Brien had made comments during an inquiry staff training session in February, including that one survivor had described being abused as the "best thing that had ever happened" to them.
Dr Claire Fyvie complained that even if this comment was meant to "lighten the mood", it was "wholly inappropriate" and demonstrated a "shocking level of misjudgement".
However, Ms O'Brien insisted that she had "done nothing wrong", saying she would "never underestimate the gravity of child abuse" and that she had "accurately reported without endorsing, what a survivor had said about their attitude to their own abuse."
She said she would resign because she had "no confidence" that the government would not simply find another reason to sack her.
Mr Swinney said he "absolutely rejects any charges of interference" with the independence of the inquiry.