The 1997 report into the separation of Aboriginal and Torres Strait Islander children from their families accused governments of genocide and called for an apology and compensation.
Members of the audience disrupted the health minister's speech at Parliament House in Canberra today, calling for the government to say sorry.
Mr Abbott continued with his speech amid heckling and audible groans from the audience.
He later told reporters that although he did not like being heckled he was pleased to have attended the function.
"No-one likes being heckled and I thought that both Mal (Brough) and I were treating the occasion with a lot of seriousness and with a lot of respect," Mr Abbott said.
"We entered into the spirit of the day and I'm a little disappointed that not everyone agreed but never the less I'm pleased to have been there."
Mr Abbott said while he could understand why Lowitja O'Donoghue wanted a government apology, the debate had moved on.
"The important thing for reconciliation is what happens in the hearts of individual people," he said.
"A lot of very good things have happened over the last generation and I would rather dwell on the good that's been done rather than engage in something that which is more likely to be debated.
"Someone like Lowitja might want to give the government a little wrap over the knuckles because sure there's always more that you can do.
"I'd rather focus on the good things that are happening and the good that has been done than go over old ground."
The government has announced 22 more staff will be employed for services to help members of the stolen generation find their families.