Customers of Australia's biggest credit union have reported money missing from their accounts after an online banking overhaul shut down some of the company's services for more than two days.

CUA suspended online, telephone and mobile banking over the weekend as it carried out the redesign.

Within hours of the shutdown on Friday night, angry customers had taken to the credit union's Facebook page.

"Unacceptable that both net and phone banking down at the same time, unacceptable that its down for entire weekend," a customer wrote.

"I would imagine weekday shut down would be less inconvenient."

Some customers said they were unable to withdraw cash from ATMs.

"I have no access to money and out for my sons birthday, so embarrassing trying to pay for movies and it is declined!" a customer wrote.

"When can I access my money through an ATM? Might of been a better idea to have at least a skeleton staff in branches this morning because there is a lot of upset people trying to use the ATM with no joy," another said.

A handful of customers reported money missing from their accounts when CUA's new online banking service began operating on Monday morning.

"There was money missing from my account which even though I put there, they said never really existed," one customer posted.

"Just like that. Not happy. I told them it was theft. They said they'd pass on my concern."

Another customer reported money missing from a home loan redraw account.

"Looks nice, but for some reason lost the money I had in my home loan re-redraw. Now says $0".

On Monday night, CUA extended the opening hours of its call centres to manage the high number of customer enquiries.

But customers reported being kept on hold for extended periods, or waiting hours to be called back.

"Still waiting for a call back! It's been about 3 hrs, usually don't have to wait on hold this long.. what's going on CUA?," a customer wrote on the Facebook page.

"I hope your not turning into one of those useless big 4s."

In a statement, CUA said it was "managing a few teething issues".

"Overall, we're happy with the performance of our national network of branches, offices and call centres throughout this implementation," the statement said.

"We will be making no further public comment until our post implementation work has progressed further."

CUA chief executive Chris Whitehead tweeted about the problems on Monday night.

"Spending the evening in CUA's Melbourne call centre, a fantastic team so committed to helping out our customers - it's great to listen to," he wrote.

"I've been asked about new online banking background - it's 1 of our new style branches - we want you feeling as welcomed online as in branch," he said in another tweet.

Some customers complained about the new layout of the online banking services.

"It's a shame CUA had to change the look of their online banking site," one user wrote.

"The old one was great and very user friendly. The new site looks terrible."

"Sorry to say this, but the new design is woeful," another customer posted.

"I don't mind a facelift, but the new layout shows LESS information at a glance and is less intuitive to navigate."

Others complimented CUA on the redesign.

"I LOVE the new site! So much easier for me to understand!," one wrote.