The federal government has released the names of organisations, including government departments, awarded grants through a controversial new Indigenous funding system. At the same time, some unsuccessful programs have been negotiating their money back.

Last month the minister for Indigenous affairs, Nigel Scullion, announced more than $860m in grants had been awarded to 964 organisations to fund 1,297 projects under the Indigenous Advancement Strategy (IAS).

The IAS is the result of more than half a billion dollars in cuts in the 2014 budget, and consolidates more than 150 Indigenous affairs programs and policies into five broad areas.

It was later revealed that 2,472 applications for 4,948 projects had been rejected, and even those that were successful were often given at best a continuation of current funding for just another 12 to 18 months.

On Tuesday afternoon a list of all successful organisations – but no breakdown of individual programs or amounts – was published on the Department of Prime Minister and Cabinet website.

The list included several state government departments as recipients of the federal funds, including various departments of education, as well as health and ageing, justice and attorney general, and sport and recreation. The “Northern Territory of Australia” is also listed.

Guardian Australia understands the NT Department of Health was granted funding for two initiatives, including sustaining Aboriginal employment in the department.

The Queensland Department of Education and Training successfully applied for a project focusing on students’ engagement, attendance and education outcomes, and the Tasmanian Department of Education for support programs increasing early childhood education participation among Indigenous families. The NSW Department of Education and Communities successfully applied to fund 87 school-based Indigenous employees in rural and remote locations.

The list also reveals a number of sporting organisations, including Australian Rugby Union, the Brisbane Broncos and North Queensland Cowboys NRL clubs, Swimming Australia and Athletics Australia.

Guardian Australia has been told the Brisbane Broncos’ project intends to mentor Indigenous year 12 students in the outer regions of Brisbane, in order to increase school attendance, improve education results, and enable transitions from school to further education or training.

Scullion said he would release the IAS funding amounts once negotiations between organisations and the department were complete.

“I made the decision to conduct negotiations in March to give my department the necessary time to make sure the funding agreements and projects deliver the long-term, sustainable results Indigenous communities want and deserve,” Scullion said.

“I have made a commitment that there will be no service delivery gaps as a result of this process. Where gaps are identified, my department will work closely with providers and communities to address those issues as a matter of urgency.”

Guardian Australia has been told by several organisations that they may not be able to accept grants because the offers are not enough to run their proposed programs, but at least one organisation has already successfully lobbied for a reprieve.

The Barkly Regional Council, which had said it would lose 27 employees after the government denied its funding request for a sport and recreation program, has been granted a 12-month continuation, Guardian Australia was told. The program provides diversionary activities to about 1,000 children in a region which has recurring issues among its youth population, including volatile substance abuse.

Scullion’s office was unable to respond by deadline to questions on where the 12 months’ reallocated funding for the Barkly Regional Council would come from.

Western Australian Greens senator Rachel Siewert said the funding remains “completely opaque” despite the publication of the list.

“This information is not complete and is therefore largely unhelpful,” Siewert told Guardian Australia.

“The government has failed to admit who did not receive funding. This is important news for the community, who need to quickly identify gaps in services. The community are also still unable to get a full picture of how much funding organisations listed will receive, for how long, and for what service.”

The list’s release comes after weeks of anger and concern among Indigenous organisations that the funding provided by the federal budget would lead to job losses and closures of frontline services.

The national Aboriginal and Torres Strait Islander legal services announced it would collapse in June after it was denied any funding through the IAS. Several others flagged job losses and axing of services.

Last week the federal Senate voted in support of a motion launching an inquiry into the IAS.

Siewert moved for the Senate finance and public administration references committee to examine the tender process and how the outcomes will impact on the efficiency and sustainability of service delivery.