OTTAWA - The federal government says it will investigate a report that scores of native children died of tuberculosis in the last century while attending residential schools.

But Indian Affairs Minister Jim Prentice is not ready to offer an apology based on the media assessment of government archival records.

"I've instructed my department to get to the bottom of this,'' Prentice said Tuesday outside the Commons.

"It is unimaginable to me that your child would go away to school and not return,'' said the father of three grown daughters.

That said, Prentice reiterated that a $2-billion compensation deal, expected to be finalized between Ottawa and former students by next September, does not include an apology.

This, despite the minister's own description of the residential schools legacy as "one of the saddest chapters in Canadian history.''

"I am astounded at the government's unwillingness to apologize,'' said Liberal native affairs critic Anita Neville.

"They have no hesitation in apologizing to other groups.''

For example, Prime Minister Stephen Harper said he was sorry for the racist head tax once imposed on the ancestors of Chinese Canadians.

"There's no good reason for not apologizing,'' said Neville's NDP counterpart, Jean Crowder. Her British Columbia riding includes several First Nations and many former students.

"You've already admitted a legal liability by compensation. I don't get it.

"And it would go such a long way to helping people move on with the next chapter of their lives.''

Prentice says Indian Affairs will work with the Catholic, Anglican, United and Presbyterian churches that once ran the schools. A truth and reconciliation commission to begin next fall will also examine the sad legacy of "disappeared children,'' he said.

"It happened over the course of close to 100 years of Canadian history. You know, the answers we get may never be totally satisfactory.

"But we'll work together with the churches ... to find out which children we're speaking of, why they didn't return and where the bodies are.''

Native people once forced to attend the live-in schools for up to 10 months each year have long talked of mysterious deaths and unmarked graves.

Archival records assessed by the Globe and Mail show as many as half the pupils who attended the early years of residential schools died of tuberculosis.

The highly contagious disease continued to spread like a scourge despite repeated warnings to the government of poor sanitation and lack of medical care.

Children passed away from TB at staggering rates for at least four decades, the report says.

Peter Bryce, the Department of Indian Affairs' chief medical officer, warned in 1907 that schools were making no effort to separate healthy children from the sick and dying.

He visited 15 Western Canadian residential schools and found at least 24 per cent of students had died from tuberculosis over a 14-year period, says the report. One school alone had a 69 per cent death rate.

The revelations come as about 80,000 surviving former students are mulling the $2-billion compensation package offering them average payments of $24,000 each.

Courts approved the sweeping deal last month. Those who attended the schools have until Aug. 20 to opt out. Ottawa can cancel the offer if more than 5,000 people decide not to accept it.

Otherwise, payments are expected to flow by November.

Churches ran the institutions across Canada for much of the last century. They started receiving federal funds in 1874 as part of Canada's plan to assimilate native people into white culture -- starting with their children.

Prentice has taken heat from Liberal MP Gary Merasty, who is native, for suggesting the schools were primarily meant "to educate'' aboriginal kids.

Lawyer Darcy Merkur of the Toronto firm Thomson Rogers said it's understandable that Prentice won't commit to an apology until the compensation deal is finalized, likely Sept. 19.

"It's a bit of a box they're in,'' he said in an interview. "If you ask that question on Sept. 20 and it's the same answer, I can understand why there may be a bit of surprise.''

Thomson Rogers represents 1,200 former students, and spearheaded the national class-action lawsuit that helped spur the federal compensation offer.

"Most of our clients are concerned with the government accepting responsibility, and I guess an apology is part of (that),'' Merkur said.

"I think it would be welcomed. I don't think it's crucial.''