National Australia Bank - whose own industry is plagued by claims it is opaque and untrustworthy - has raised concerns that the Northern Australia Infrastructure Facility, a controversial government loan scheme designed to kickstart private sector investment in the north, lacks transparency.

NAB also warned that the fund was taking a "lender of last resort" approach that may not provide the economic shot-in-the-arm that Northern Australia requires.

The bank's concern adds to a chorus of complaint that the much-vaunted infrastructure fund, which headlined the 2015 federal budget, is cloaked in secrecy, lacks governance and exposes taxpayers to a high risk of losing their money.

The Productivity Commission has warned of possible political interference in the fund's investment decisions, and former treasurer Wayne Swan described it as a government "slush fund" operated by a board stacked in favour of the mining industry.

Among projects being considered by the fund is a contentious rail link from the proposed Adani coal mine in Queensland's Gallilee Basin to the Abbot Point coal port, near the Great Barrier Reef.

The Northern Australia Infrastructure Facility has refused to comment publicly on projects it is assessing, or applications it has received.

In a submission to a Senate inquiry into the facility, NAB said it supported NAIF, and believed protecting a client's confidential information was paramount. But it said the fund's confidentiality practices must be "balanced with the public's interest in NAIF's developments".

"NAIF could consider creating a more transparent transaction pipeline to assist building momentum in projects" under evaluation, the submission stated.

At a Senate hearing this month, the Northern Australia Infrastructure Facility chief executive Laurie Walker said its confidentiality procedures were in line with that of other lenders, and that the Australian Government Solicitor reviewed the facility's core governance and found it to be "best practice".

Australia Institute researcher Tom Swann told the hearing that while the Infrastructure Facility repeatedly cited the need for confidentiality surrounding potential projects, former Resources Minister Matt Canavan, Deputy Prime Minister Barnaby Joyce and Queensland Premier Annastacia Palaszczuk "have all repeatedly supported a large concessional loan [from the facility] to Adani for its rail line - including at a press conference with the Australian head of Adani".

In April, Mr Joyce reportedly rejected suggestions that the fund was a lender of last resort, despite 14 banks and financial institutions having refused to provide finance to Adani.

But in its submission, NAB claimed the Northern Australia Infrastructure Facility's investment mandate did entail a "lender of last resort" approach, which "may not be sufficient to accelerate investment".

"A more proactive approach could initiate more NAIF funded projects," the submission stated.

A spokesman for Mr Joyce on Thursday said he was "confident the NAIF is working within a robust and appropriate framework, but will consider findings from the inquiry on their merits".

Labor's Northern Australia spokesman Jason Clare said Labor was "deeply concerned" about the fund's governance, adding it had "spent more money on executive salaries and travel perks than it has on Northern Australia".

A NAIF spokeswoman said it understood NAB's comments "regarding assisting potential financiers around creating awareness of potential projects", and that NAIF works with proponents, when appropriate, to "make introductions to other financiers and advisers where they may be able to assist with a project".

She said NAIF's commercial-in-confidence procedures were "in the public interest" as they enabled NAIF to maximise the public benefit in its negotiations.

Australian Conservation Foundation campaigns director Dr Paul Sinclair said the Northern Australia Infrastructure Facility was "shrouded by secrecy" and "created to bankroll Adani's massive dirty coal project, which would help accelerate the decline of our Great Barrier Reef and further pollute our planet".