Private sector outfit Pillar Administration, hired by the Commonwealth Superannuation Corporation to manage payments, is struggling to integrate a new computer system and members of the PSSap fund have been the losers.

Public servants at the giant Defence Department have been hardest hit with up to 6700 employees at the giant department missing payments received on March 9, March 23 and April 6 with the money not allocated until April 10.

Contributions to workers at the Department of Human Services, the Australian Bureau of Statistics and Department of Foreign Affairs and Trade are also affected, "impacting one or two fortnightly contributions", the corporation told Fairfax.

CSC says the money in question is only a tiny proportion of the payments it handles each month and that the majority of the PSSap's 135,000 members are unaffected.

But one Defence Department workplace union says the mess is another example of the dangers of public sector outsourcing to private firms.

A spokesman for the corporation told The Canberra Times that the problems had been identified and "remedial action" had been taken.

"There has been an issue with the processing and allocation of some PSSap superannuation contribution payments," the spokesman said in a statement.

"The problems have been identified and remedial action has and continues to be undertaken

"PSSap member accounts will reflect contributions and earnings from when contributions should have been made

"CSC is in discussions with Mercer and Pillar about solving any remaining issues."

The CSC spokesman said Pillar had moved its PSSap work onto a new administration platform late last year.

"Since transition, there have been some issues allocating contribution payments to members' account," he said.

"For the most part issues surrounding contribution allocation have been managed in a timely way with minimal member impact.

"Contributions from the Department of Human Services, Australian Bureau of Statistics and Department of Foreign Affairs and Trade are also affected, impacting one or two fortnightly contributions.

"A number of PSSap member accounts from those three agencies have outstanding contributions, a significant number of these accounts will be allocated shortly.

"Overall, PSSap has 135,000 members and allocates around 200,000 contributions each month.

The corporation said just over 1 per cent of total annual contributions, about $11.4 million, were unallocated, including $5 million worth of contributions received in the last six days which are being processed normally.

"The contribution allocation delays have been caused by a variety of issues in the format or nature of data included in contribution files from employers," the spokesman said.

"For example, one of the issues was related to the format, or omission, of some Tax File Numbers."

One Defence Department workplace union, Professionals Australia, was not impressed with union official Dave Smith said the glitch was another example of outsourcing going wrong.

"It shouldn't be up to employees to check whether this has been fixed," Mr Smith said.

"CSC, or their external "service provider", should be upfront with employees who have been affected and clearly communicate how they are going to make good on their mistakes.

"It's also time that government had a good, hard long at the endemic systems failures we are seeing across Government service and properly invest in enough in-house expertise and oversight."