Dr. Charles Smith gave a tearful apology on Thursday to an innocent man who spent 12 years in prison for the death of his niece, a conviction based largely on the disgraced pathologist's testimony.

When the lawyer representing William Mullins-Johnson asked Smith if he would apologize to his client, it triggered an emotional exchange.

"Sir, I don't expect that you would forgive me," Smith said, fighting back tears.

"But I do want to make it very clear to you that I am profoundly sorry for the role that I played in the ultimate decision that affected you."

Standing only metres away, Mullins-Johnson stood up and struggled to compose himself for nearly a minute before he spoke and forgave Smith.

"You (put me in a place) where I could have been killed any day for something that never happened," he said. "My brother's relationship with me, and my niece that's still living and my nephew's that still living, they hate me because of what you did to me.

"I'll never forget that, but for my own healing ... I must forgive you."

Smith replied: "That is kind of you, thank you."

Mullins-Johnson spent 12 years in prison after being convicted of raping and murdering his four-year-old niece. Several experts later found no evidence to indicate the girl was sodomized and asphyxiated.

Last year, the Ontario Court of Appeal quashed his conviction.

After the dramatic exchange, Mullins-Johnson told CTV Toronto that forgiving Smith will help him find inner peace.

"I know that if I didn't forgive him, my fear was that I wouldn't be able to get on with my life and get past this, and the anger that I feel about this whole situation would eventually burn me up," he said.

Later in the day, lawyer James Lockyer, who represents several wrongly accused individuals affected by Smith's work, asked if the pathologist "enjoyed sticking the knife in, so to speak," in his role as an expert witness.

"That is absolutely -- excuse me for interrupting -- that is absolutely false," Smith said, raising his voice for the first time during his testimony. "There is no enjoyment in this whatsoever.

"Anytime I testified in court it was a tragic situation ... I always knew them to be tragedies."

In May 1999, one month before second-degree murder charges were withdrawn against Brenda Waudby in the death of her 21-month-old daughter, Smith was informed by the Children's Aid Society that Waudby had given birth to a baby boy.

"Well, I guess I'll be doing his autopsy too," Smith was recorded as saying in a CAS letter.

On Thursday, Smith said he has no recollection of making the comment.

"I had never prejudged the criminal charge in that case," he said.

Outside the inquiry, Waudby said the comment caused her to "cry for days."

"It's disgusting the way he acted," she said.

Smith offered a general apology on Monday before he began testifying at the Goudge inquiry, but Thursday was the first time he apologized directly to one of the people affected by his work.

Earlier in the week, Smith testified his training as a pathologist was "woefully inadequate" and he was basically self taught. He also admitted he was "ignorant" of how the criminal justice system worked, saying he believed his role was to give evidence that would support the prosecution.

Smith's findings in 20 cases of suspicious child deaths are the subject of the inquiry into systemic failures in the practice of pediatric forensic pathology.

Smith is expected to conclude his testimony on Friday.

With a report from CTV Toronto's John Musselman and files from The Canadian Press