Panicked pensioners tried in vain to call the corporation from Wednesday evening trying to find out what had happened to their money, but the phones were not answered and the agency's website crashed.

It is unclear how many of the hundreds of thousands of Australians who rely on government super payments have been affected, with CSC failing to answer the question on Thursday.

But the corporation blames a glitch with their bank, Westpac, which was being fixed but conceded that pensioners still might be waiting for their money on Thursday evening.

Several retirees told Fairfax this was the first time in their long experience when they had not been paid on time and one pensioners group told of its members' dismay at the failure.

The CSC is the trustee of nine superannuation schemes, including the Commonwealth Superannuation Scheme and the Military Superannuation and Benefits scheme.

Payment problems were reported by members of the PSS, CSS, the DFRDB and MilitarySuper funds.

The Superannuated Commonwealth Officers Association, which represents retired public servants, told Fairfax it was "extremely important" that pensions were paid on time.

The association's ACT branch president, Ewan Hazell, told of the dismay among retirees when they realised they had not been paid.

"It's extremely important," Mr Hazell said.

"It's the one given, in any sort of work or pension situation, that you expect that it will be there when it is supposed to be there.

"Association members have been very dismayed that this has happened."

The former public servant, whose own pension had been paid without incident, said the most common consequence of the mess would be some inconvenience, but for some retirees it might have serious affects.

"In some cases something quite major could come of this, let's hope not," Mr Hazell said.

"Let's hope this is a one-off, they get it nailed down and it never happens again."

Assistant Defence Minister Stuart Robert moved on Wednesday to assure those in the Defence community affected by the glitch that every effort was being made to get their money to them.

"Resolving this problem is the priority for CSC, which is working with Westpac to rectify the issue as soon as possible," the junior minister said.

The CSC itself apologised to fund members and said it was working hard to get payments out as soon as possible.

"Commonwealth Superannuation Corporation apologises for any delay that has occurred," the organisation said in a statement on Thursday.

"Our bank has advised that they are completely focussed on having all payments processed to pensioner accounts as soon as possible.

"Many payments, particularly those to the major banks, have been credited to accounts.

"They expect to see the balance of such payments effected from 1pm this afternoon, with the remaining accounts at the affected other banks and credit unions following during the afternoon.

There is a chance that some payments may not hit pensioners' accounts until tonight – our bank is working to quantify this potential and to speed up the payments wherever possible."

Correction: An earlier version of this article referred to ComSuper. ComSuper ceased to exist on July 1.