The central bank said the system, known as Osko, that allows customers to transfer money rapidly between banks, experienced an "internal engineering issue" on Wednesday.
"The RBA experienced an internal system engineering issue yesterday evening," the bank posted to Twitter.
"The issue has now been contained. Impacted external services are now operational however there has been some delay to overnight processing of payments."
Big banks including ANZ, Commonwealth and Westpac copped the fund transfer outage.
Westpac said it was aware of an issue identified by payment platform operators that was impacting all Australian financial institutions.
"Please know that this has since been resolved," the bank said late on Wednesday.
ANZ released a similar statement saying it was "experiencing an industry-wide outage" preventing the processing of payments.
Commonwealth was also rocked by the issue impacting Osko payments.
"Please don't retry your transaction," the bank advised.
The Osko payment system was introduced to allow near-immediate online bank transfers around the clock.
It allows users to plug in phone numbers and emails to send money rather than bank details.
Meanwhile, private health insurer Medibank has also experienced a cyber attack, finding unusual network activity on Wednesday.
There's no evidence any sensitive data was accessed and Medibank reported the incident has been contained, but customers will experience some disruption as some of its systems are temporarily taken offline.
Medibank chief executive David Koczkar admitted it was a concerning development given the recent spate of cyber attacks.
"We recognise the significant responsibility we have to the people who rely on us to look after their health and wellbeing and whose data we hold," he said.
"We are working around the clock to understand the full nature of the incident, and any additional impact this incident may have on our customers, our people and our broader ecosystem."
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