A multi-million-dollar financial scandal has been uncovered at Queensland Health.

Police are seeking Health Department executive Joel Barlow over a $16 million budget anomaly.

Premier Anna Bligh says the money went missing over recent years, but $11 million has allegedly been stolen in the past fortnight.

It is believed sums of money that appeared to have been transferred to service providers were actually being transferred to a private account.

Police say Mr Barlow, also known as Hohepa Morehu-Barlow, has several aliases and has business interests separate to his work as a finance manager in Queensland Health's community services branch.

Ms Bligh says it is probably the biggest single fraud in the history of the public sector in Queensland.

She says the Government was tipped off about the fraud late on Thursday after a departmental officer noticed a discrepancy in payments.

"I can't say enough how angry I am about this circumstance," she said.

"These are funds that belong in our hospitals and in our healthcare system and for somebody to steal them is an extraordinary breach of trust that every Queenslander should be angry about."

She says no stone will be left unturned to apprehend Mr Barlow.

"If the allegations are true, this man has defrauded all of Queensland and he will face the full force of the law," Ms Bligh said.

Ms Bligh says more details of the case will be released when it is over, but Opposition Leader Jeff Seeney wants information now.

"Another $16 million of Queensland Health money has gone missing. It follows on from a whole series of incidents in Queensland Health where millions and millions of dollars have been wasted," he said.

An independent audit will be carried out to try to find out why the theft went undetected for so long.

But Mr Seeney says a serious failure is already obvious.

"This is indicative that the whole administration of Queensland Health has broken down. The financial management of Queensland Health is obviously woeful when $16 million can go missing."

Assets frozen

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Police believe Mr Barlow may be in the south-east Queensland area and urge anyone who may know his whereabouts to contact them on CrimeStoppers on 1800 333 000.

Mr Barlow, who last attended work on Thursday, was investigated for internal fraud about 12 months ago but the claims were not substantiated, Health Minister Geoff Wilson said.

Police say they have applied to freeze his assets, which include a luxury inner-city unit and several luxury cars including a Mercedes.

Deputy Commissioner Ross Barnett says police have been trying to locate Mr Barlow since Thursday night.

"As the Premier says, action has been taken today with the assistance of the CMC confiscation unit to restrain a number of assets that were under the effective control of Mr Barlow, and we await his location before we can take the investigation further," he said.

"Could I appeal to him to contact police at the fraud squad and come in for an interview," he said.

"Alternatively, anybody who may know his whereabouts to contact police either through Crime Stoppers or direct to the fraud squad."

The scandal caps a rocky few years for Queensland Health, which has been beset with payroll problems.

It was only today that it was revealed the department was going to go after small amounts of money - around $200 - which it has overpaid people.