Opposition Leader Bill Shorten demanded to know how, given the report's findings, the government could justify cutting $500 million from indigenous affairs.
Mr Turnbull said while there had been "substantial progress" in improving the lives of indigenous Australians he acknowledged there "is much more to be done".
"The proposition that the government is cutting funding for indigenous affairs is simply wrong," he told parliament.
"We are putting more resources into indigenous advancement all the time."
Mr Turnbull late last year announced a "refresh" of the Closing the Gap strategy after the ninth annual report card on its seven key targets found that just one was on track to be met.
He met with indigenous leaders in Canberra this week and would discuss ways to improve and expand the strategy when he meets with his state and territory counterparts on Friday.
Details about the refreshed strategy were due to be announced Monday when Mr Turnbull unveils the 10th annual report card on progress toward closing the gaps in life expectancy, child mortality, education and employment.
Mr Turnbull said the refreshed strategy would include "more extensive" targets, with state and territory governments being called on to help close the gap.
A Close the Gap steering committee report said the government's strategy had all but fallen apart and a funding boost for indigenous health was needed to meet the target of closing the 10-year life expectancy gap with non-indigenous Australians by 2031.
Mr Turnbull attended a breakfast launch of the report at parliament house but was criticised by Labor senator Pat Dodson for leaving before it concluded.
"It's indicative of the deafness, the absolute derision and the contempt which this government is meting out to the Aboriginal people," the senator told reporters.
It is understood organisers were aware of Mr Turnbull's schedule and that he would leave at the time he did.
CLOSING THE GAP TARGETS
* Halve the gap in child mortality by 2018
* Close the gap in life expectancy by 2031
* To have 95 per cent of all indigenous four-year-olds enrolled in early childhood education by 2025
* Close the gap in school attendance by the end of 2018
* Halve the gap in reading and numeracy for indigenous students by 2018
* Halve the gap in Year 12 attainment by 2020
* Halve the gap in employment by 2018