Nick Xenophon says Defence's military and public service chiefs must put systems in place to cope with a rising tide of reports of misuse of public funds.

Fairfax has uncovered yet more reports and allegations of rorting of Commonwealth credit cards, regimental funds and other entitlements both in the military and civilian defence operations.

In one case, Defence is investigating the disappearance of files from a secure military archiving facility in Sydney, with the documents allegedly stolen to cover up the rorting of money from the regimental funds of an elite commando unit.

A group of DSTO technicians were "counselled" last month after they paid for a dinner in Adelaide - washed down with 29 bottles of wine - with a Commonwealth cards and then tried to claim meal allowances for the evening of the spread.

One former Defence Ministerial staffer confirmed that cultural issues in Defence were on the radar screens of senior politicians.

"There is a sense of entitlement to taxpayers' money among some people at Defence, maybe it's because they see themselves as the department that doesn't get out of bed for less than half-a-billion bucks," the former aide said.

Senator Xenophon, who has been pursuing the issue through questions on notice to the Defence Department in Senate committees, told Fairfax Media he believed there was a widespread problem in Defence and its approach to protecting public money.

"If you don't have the mechanisms in place then you are asking for trouble," the Senator said.

"I'm not saying that people in Defence are anything other than overwhelmingly honest but when you have a lack of systems in place it is concerning.

"There must be adequate and robust systems in place and I don't think those processes are in place at this stage.

"I worry that there is a systemic problem, that there are inadequate safeguards in place to deal with this, that if there are any bad apples in Defence, it's much easier for them to get away with it."

The defence department has launched an internal inquiry into suspected misappropriation of tax payer funds involving one or more members of the army's elite 2nd commando regiment.

The suspected financial malfeasance was discovered after a confidential file detailing the use of regiment funds was removed- without approval - from defence department archives at Sydney's Randwick Barracks .

Subsequent searches for the missing file have proved fruitless, sparking internal complaints that it has been stolen to cover up the misconduct.

The missing file contains details about the expenditure of thousands of dollars in regimental funds allegedly spent on inappropriate items.

Defence's MediaOps unit had not responded by deadline on Tuesday to questions on the alleged incident.

The department has also not responded to reports that a group of Defence Science and Technology Organization staffers were recently caught trying to claim meal allowances for a night away on business in Adelaide.

But The Canberra Times understands that the boozy evening  - when 14 public servants drank 29 bottles of wine were –  had already been paid for with a Defence-issued credit card.

Almost 70,000 public servants and uniformed personnel working for the Defence Department and Australian Defence Force have access to cards which in total can rack expenses of more than half-a-billion-year.

But the use of credit cards by Defence personnel and public servants has made news in Canberra twice this month with both civilians and soldiers sacked or disciplined over unauthorised spending.

Senator Xenophon said he wants to see changes to way the Defence establishment approaches allegations of fraud or misappropriation of funds.

"There needs to be independent oversight and there should be process that are as robust as possible that can be subject to independent scrutiny," he said.

"If somebody has a complaint about fraud then those complaints should be taken seriously and investigated thoroughly."