The calls came as Prime Minister Tony Abbott prepared to deliver his annual report to Federal Parliament on Wednesday on progress towards the six targets.

"My message is not to take the foot off the pedal at this crucial time, when we've seen small but significant gains," said Kirstie Parker, co-chairwoman of the Close the Gap campaign.

"Where there've been cuts or there is uncertainty around funding to health and related services, that has to be reversed, the funding has to be restored, so the considerable investment we've seen to date as part of a bipartisan effort is not squandered," Ms Parker said.

A report to be released by the Close the Gap campaign on Wednesday calls for a significant ramping up of primary healthcare services to detect, treat and manage chronic conditions such as diabetes and kidney disease.

The campaign also urges the government to restore $130 million cut from a program to tackle Indigenous smoking, and to better co-ordinate efforts to improve Indigenous health with the government's Indigenous Advancement Strategy, which focuses on education, employment and community safety.

"Without good health, our people can't engage with education or employment, so they can't be separated," Ms Parker said.

Aboriginal and Torres Strait Islander Social Justice Commissioner Mick Gooda, another co-chairman of the campaign, said the $4.8 billion Indigenous Advancement Strategy, in which 150 Indigenous programs have been consolidated into five broad areas was  a "shambles".

Hundreds of organisations will have to wait until March to find out whether they will receive funding under the program beyond June 30.

"We're now all anxiously holding our breath," Mr Gooda said. "Without the certainty of which mob are being funded and which mob aren't, it's certainly causing problems."

He called the cuts to anti-smoking programs "the worst form of short-termism," and warned that proposals to cut Medicare rebates for GP visits by non-concessional patients by $5 would represent a barrier to Indigenous people seeking care.

National Aboriginal Community Controlled Health Organisation chairman Matthew Cooke called on the government to end the funding uncertainty for Aboriginal health clinics, which don't know what funding they will receive beyond June 30.

"The government needs to stay the course if we're serious, and if we're genuine about closing the gap," Mr Cooke said.

The Assistant Minister for Health, Fiona Nash, said the government was committed to ongoing funding for primary healthcare services for Aboriginal and Torres Strait Islander people.

"I'm aware that services are keen to know about funding as soon as possible to ensure certainty and good planning. I am confident we will be able to inform organisations about funding arrangements soon," she said.