Police investigating corruption claims against a senior WA public service executive now say as much as $25 million may be involved in a false invoicing scheme that took place over several years, a court has been told.

Key points: Charged executive Paul Whyte and another man faced court today

Charged executive Paul Whyte and another man faced court today Attorney-General John Quigley said the investigation was "very large and serious"

Attorney-General John Quigley said the investigation was "very large and serious" He encouraged public servants to come forward and tell police what they know

Department of Communities assistant director general Paul Whyte, 56, was on Thursday charged with two counts of official corruption after a joint WA Police and Corruption and Crime Commission (CCC) investigation.

A second man, Jacob Daniel Anthonisz, 43, who is not employed in the public sector, was also charged.

WA Police originally said the amount being investigated was more than $2.5 million, but this amount was dramatically increased during the men's first appearance in the Perth Magistrates Court on Friday morning.

Paul Whyte appears at Perth Magistrates Court for the first time since his charge. ( ABC News: Hugh Sando )

It is alleged the pair created false invoices and then transferred the money into company bank accounts before withdrawing it for personal use.

The court was told each single amount was allegedly just below $50,000, to avoid the requirement for higher approval within the Department of Communities.

Paul Whyte faced a barrage of questions from the media outside Perth Magistrates Court. ( ABC News: Hugh Sando )

The funds were allegedly paid to two companies, Quadrant Analytics and iValuate, which were not approved for the work purportedly carried out.

They were then allegedly used for personal expenditure and bills, and for a horse stud in New Zealand.

The court was told the pair's long-time friendship extended to ownership of racehorses.

Jacob Daniel Anthonisz was charged along with Mr Whyte. ( Supplied: Kisses in Chaos )

Alleged corruption over more than a decade

The court heard police were investigating whether false invoicing totalling $20 to $25 million had taken place going back to 2008, associated with Mr Whyte's previous roles as general manager of the Department of Housing and executive director of property registry agency Landgate.

The police prosecutor told the court he had worked as a public servant for 25 years.

Mr Whyte, who has been suspended from his senior executive position, and Mr Anthonisz were both granted bail.

Jacob Anthonisz appears in court after being charged with corruption offences. ( ABC News: Hugh Sando )

The prosecution had opposed bail for both men, arguing Mr Whyte was a flight risk and could influence current and former employees.

The pair had to surrender their passports and both are scheduled to appear in court again next month.

Paul Whyte's house in the exclusive Perth suburb of Mosman Park was the target of police raids. ( ABC News: Rick Harvey )

The charges followed a raid on Mr Whyte's house in the leafy western Perth suburb of Mosman Park, which according to property records was bought for $2.9 million in 2012.

WA Attorney-General John Quigley on Friday described his outrage and anger at the charges.

Mr Quigley said he was limited in what he could reveal, but he said West Australians would know more once the investigation was completed.

"The public is going to have to be patient because this is very, very large and serious," he said.

"This is the start of the investigation, not the end of it."

Public servants urged to tell all

Mr Quigley said the investigation would aim to trace any corruption back to its roots.

The department's annual report said Mr Whyte was "responsible for internal governance, standards and integrity" in his role.

"The person who was doing the checking, it's alleged was the fraudster," Mr Quigley said.

Paul Whyte is alleged to have stolen millions over two years. ( ABC News )

He encouraged public servants to come forward and assist the CCC with its investigation.

"I advise any public servant with knowledge of this, or any public servant with knowledge of corruption, to contact the CCC this morning," he said.

"A list is being prepared of people to examine.

"It is best to go to the CCC today."

WA Premier Mark McGowan described the allegations as "appalling" and said the Public Sector Commission would launch an independent review into the claims, in addition to the CCC investigation.

"If proven, these allegations are absolutely appalling and will be a complete betrayal of every West Australian," he said.

"I know people across the community do a great job and often don't get paid a lot of money for it, and every West Australian would be shocked and outraged by these allegations."

Mr McGowan said legislative changes introduced in 2018 had given the CCC the powers it needed to pursue the allegations, including unexplained wealth provisions which allowed for the freezing of assets.

Department of Communities director General Michelle Andrews said an interim replacement was being appointed to replace Mr Whyte. ( ABC News: James Carmody )

Department of Communities director general Michelle Andrews said she was "disappointed" by the allegations.

"I have been the director general of the Department of Communities for just over six months and have found the Department of more than 6,000 outstanding employees to be dedicated and committed professionals," she said.

Ms Andrews said she had taken steps to appoint an interim replacement for Mr Whyte from outside of WA.