A bank client based in Sydney told ZDNet Australia the machines were unable to process transactions.
A recorded message on EDS' helpdesk setup especially for the bank's employees said: "This is an EDS announcement. We are currently experiencing problems with ATMs not being able to process transactions."
"This is being investigated as a priority," the message said.
An EDS spokesperson said the ATMs had been down for "a short period of time", but refused to say when the problem first started.
The matter had since been rectified, she claimed, and had affected "only a small number of ATMs".
However, a Commonwealth Bank spokesperson said about 250 machines faced problems between 2:45pm and 3pm (AEST).
"There was a group of ATMs all out together and during this time, the machines were offline and could not be operated by customers," he said.
The problem was caused by "a software issue" in the ATM host system. EDS was investigating the cause of the problem, he added.
A check at 5pm (AEST) revealed there was no change to EDS' helpdesk recorded message.
The blunder comes as the Commonwealth Bank recently moved to wind down its 10-year, AU$5 billion technology services contract with EDS, originally signed in 1997. The bank recently sold its 35 percent holding in EDS Australia [to EDS], saying it no longer considered the investment as core to its business.