A lawyer who spent more than 30 years at the Immigration Department says there has been an exodus of senior staff from the newly formed Home Affairs organisation, and that there are deep problems within Australian Border Force (ABF) as its Commissioner remains under investigation.

Commissioner Roman Quaedvlieg has accrued about $500,000 in salary payments since going on leave in May last year, when an external investigation began into his personal conduct.

Greg Phillipson, who resigned as a senior Immigration Department lawyer in June last year, says his former colleagues have described an organisation that is now in crisis.

Sorry, this video has expired Greg Phillipson says former colleagues have told him Border Force is "a shambles".

"There's a lot of concerns held within Border Force about whether it's structured appropriately, whether it's working well as an organisation," Mr Phillipson told 7:30.

"Some people have described it very recently to me as a shambles."

Mr Phillipson said members of the Australian Border Force, which was formed in 2015, are openly acknowledging the problems within the organisation, which has been without its Commissioner for nine months.

"It certainly really has contributed to uncertainty within the Border Force and the lack of leadership at that very high level is unsettling," Mr Phillipson said.

The retired lawyer says many experienced staff have now left the Home Affairs Department, which only began operating in December.

"Either they were pushed or they voted with their feet, and I'm talking about the senior echelons of the department," he said.

Greg Phillipson's claims have been dismissed by the ABF.

"The claims made by a former employee of the then Department of Immigration and Border Protection in relation to the current state of affairs within the Australian Border Force are unfounded and uninformed," an ABF spokesperson told 7.30.

"Our officers do an outstanding job each and every day to protect Australia's border and the community.

"At no point has the work of the ABF slowed down and any claim the agency is a 'shambles' is not borne out by the facts.

"Over past 12 months, as the ABF has transitioned into the Home Affairs portfolio, we have seen record seizures at the border and the processing of a record number of international passengers, mail and air cargo.

"Over the same period we established a new SES team which has significantly enhanced the diversity of the ABF leadership, and continued to support our professional, dedicated and diligent officers at the front line."

Decision on Quaedvlieg's fate expected 'shortly'

Home Affairs Minister Peter Dutton (r) will not be required to make a decision about Roman Quaedvlieg's future. ( ABC News: Avani Dias )

After two separate inquiries into Mr Quaedvlieg's personal conduct, his future now rests with new Attorney-General Christian Porter.

Prime Minister Malcolm Turnbull has expressed his frustration with the protracted and expensive investigation.

"I'm disappointed the matter has taken so long to be resolved but as you can understand, it's a matter that has to be dealt with by public service processes," he said in Canberra.

"The report on Mr Quaedvlieg's circumstances is with the Attorney-General and I expect him to make a decision on it shortly."

In a statement to 7:30, Mr Quaedvlieg said he also hopes there's a speedy resolution to the situation.

"I appreciate and understand the extensive media and public interest in this matter, not the least of which is the length of time the investigation has taken, a concern that I obviously share," he said.

"My preference is to allow the Attorney-General to consider the material that is before him and make an objective decision on that material.

"I will make further public statements at the conclusion and conferment of his decision."