A former employee of a Catholic credit union allegedly stole more than $1 million from its members over a number of years.

The Serious Fraud Office and the police have begun investigating the allegations of employee fraud at the Hibernian Catholic Benefit Society following a complaint on Friday.

The friendly society has assets of $9.6 million and about 2800 members. Its credit union offers a range of financial services and mutual assistance to its members, including loans, life assurance, medical and household insurance.

Chairman Mike McBride said he was "absolutely devastated" when he discovered that a substantial amount of money was missing.

"We're extremely disappointed. I would imagine the other members would also be as gut-wrenched as I am.

"When we discovered what appeared to be going on, it was hard to comprehend. To say I was surprised is an understatement of the year."

Mr McBride said the "trouble broke" when the society's secretary was preparing for an audit of the credit union at the beginning of last month.

"He picked up a printout and thought, 'Uh oh, this doesn't appear right', and made some deeper investigations from that and the police were notified."

A former employee is suspected of taking the money over a number of years but Hibernian has not yet established the scale of the alleged fraud.

A letter was sent to all members of the society this week informing them of the investigation.

SFO director Adam Feeley said the alleged fraud potentially affected a large number of members and he could not accurately quantify the total.

"But we believe it to be at least a six-figure sum, if not a seven-figure sum."

He said the SFO would go through records over the next few weeks and analyse the data before deciding whether charges would be laid.

The investigation was receiving the full co-operation of the society's management and board, Mr Feeley said.

"Given the information that we've already received, the scale and how the alleged offending may have occurred seem to be reasonably clear. So we're already well advanced into the investigation."

Police say they are assisting the SFO in determining the extent of the alleged fraud and their combined resources will have the matter resolved in a short time.