After two days of meetings, the Northern Land Council's full council has decided to launch a second investigation into the finances of a subsidiary company.

Key points: It stems from a row over the rent paid to the Aboriginal Investment Group, where NLC executives sit on the board

It stems from a row over the rent paid to the Aboriginal Investment Group, where NLC executives sit on the board The NLC says conflict of interest allegations have now been dismissed

The NLC says conflict of interest allegations have now been dismissed The review is to be funded by the Federal Government and report by May

The extraordinary full council meeting of the organisation's 83 members was triggered by the Federal Indigenous Affairs Minister Nigel Scullion, who used his powers to hold it so questions could be asked about the allegations.

Some angry members had hoped the executive council would be removed by a resolution to the council, but that did not happen.

Instead the 83 councillors voted to launch an external forensic investigation into the allegations about the finances of the NLC's subsidiary company, the Aboriginal Investment Group (AIG).

"This is a positive outcome which sets AIG up for the future," NLC's acting chief executive Jak Ah Kit said.

"The review will result in improved operations and reporting, and consideration of options for structural reform."

The conflict of interest allegations and the investigation into AIG's finances, were sparked by a row over the rate of $1 million in annual rent the council pays to AIG, for its Darwin offices.

That's because seven NLC executive members sit on AIG's board.

Acting CEO Jak Ah Kit said the second investigation was a positive outcome. ( ABC News: Jane Bardon )

Initial audit uncovered personal loans

Last month an internal NLC committee investigated the allegations but made no recommendations on action.

The committee also reported that two serving dual board members, Samuel Bush-Blanasi and Helen Lee, and one former dual board member, Bill Risk, took out personal loans from AIG.

Mr Risk told the ABC that the loan to him was taken "at arm's length", that he did not involve himself in the decision, and that he would pay the $86,000 back.

The committee found the NLC had no way of knowing what AIG had spent $4 million of Federal Government money on, which it was provided in 2012 by the NLC.

It also probed AIG financial reports and audits that suggested the charity arm of AIG had given $3.9 million in loans to its commercial arm.

The full council dismissed the conflict of interest allegations against the NLC executive over the leasing of its Darwin offices.

It passed a resolution saying that "executive council members properly and appropriately handled perceptions of a conflict of interest in relation to the leasing of the NLC Darwin office, due to being AIG directors".

"Three legal sets of advice have told us there's no conflict of interest," Mr Ah Kit said.

"And the full council is pleased that that issue has been put to bed."

Senator Scullion said he was happy with the outcome of the meeting.

"All of the council members want to know exactly what's going on," he said.

"So this audit and the breadth of the terms of reference will allow that."

Nigel Scullion was satisfied with the outcome of the meeting. ( ABC News: Jane Bardon )

'Sad day for democracy'

But several regional councillors including John Daly from the Daly region told the ABC they were not satisfied.

"To me it's just a sad day for democracy as far as Indigenous people are concerned," Mr Daly said.

"This is going to continue on and the quagmire won't go away."

Darwin councillor Paul Henwood said he said he remained angry about the dismissal of the former chief executive Joe Morrison, who raised the allegations, and had been brought into the NLC in 2014 to fix previous governance problems after a critical National Audit Office report.

"Joe was a main player in raising concerns, and correcting them in the past. He came into the NLC when it was $13 million in debt, and left it in surplus," Mr Henwood said.

'No conflict'

The executive members refused to speak to the ABC during or after the meetings over two days.

But they have previously denied they are conflicted.

The chief executive said the personal loans taken out by executive members Mr Bush-Blanasi for $1,665 and Ms Lee for $2,347 had been repaid to AIG.

Mr Ah Kit said the $4 million in federal money provided to AIG was spent properly on remote community projects across the Northern Territory.

Senator Scullion said the Federal Government would fund the new investigation and it would be complete in time for the next full NLC meeting in May.

"We need full financial reports from the subsidiaries, some of these answers to the question about millions, or lots and lots of money that has been loaned and has apparently yet to come back," he said.

But Senator Scullion said he was confident the second investigation would not cause a delay with negative effects.

"They're going to have a full forensic audit, it's going to be available for everybody and I don't think that anyone can take from that that there'll be any governance problems festering in between," he said.

Police called for a second time

The meeting was heated and for a second day in a row the police were called by the Land Council's chief executive to assist in expelling some angry members.

Senator Scullion told two carloads of officers who arrived at the Darwin venue their help was not needed.

"They certainly weren't needed and they left. So I'm not sure what that was completely to do with," he said.

He said it was crucial to him that the Land Council resolved its internal disputes because he wanted to keep working with it on projects including remote housing delivery.

"This is one of the most important organisations in the Northern Territory. This is the parliament for the north of Australia for Aboriginal people," he said.

Darwin councillor James Sing said it would be crucial that following the second investigation the NLC shows it will address any governance problems, if confirmed.

"If we don't stand up now and show Aboriginal people, not only in our region, but in the wider population, that we respect governance, and we are not going to take issues that risk our organisation in any way, there could be long-term implications for our members and the communities," Mr Sing said.

'AIG may look to repay funds'

The AIG's chief executive told the ABC that some of the $3.9 million that the organisation provided from its charity arm to its commercial arm may be repaid.

"In terms of the repayment of funds it was always the case that the parent company may look to pay back funds when it is reasonably necessary," Steve Smith said.

He said the money had been used by AIG's commercial arm to take over struggling Indigenous businesses and manage them back to financial health, as well as to develop other projects from scratch.

"Those sorts of operational expenses allow for us to deliver projects within the region," he said.

"I mean the community store in Barunga is one example, the store in Timber Creek is another example."

The AIG's chief executive Steve Smith has told the ABC that some of the $3.9 million that the organisation provided from its charity arm to its commercial arm may be repaid. ( ABC News: Jane Bardon )

Mr Smith said $1.09 million of the money the group's charitable arm put into a Timber Creek tourism accommodation, Wirib Tourism, five years ago would not be recovered.

"The funds put into Wirib Tourism Park were an operational expense and they went into items to support that park at the time around things like vehicles, forklifts, upgrades to water," he said.

"Had we not gone in with that substantive investment that site would have closed. It is now worth $4 million."

He said the group had also completed three houses it rented in Katherine, a wind and solar test tower in Gove, had helped an Arnhem Land Indigenous corporation take over a former Rio Tinto quarry, and now had $18 million in assets.

