Is your superannuation balance looking a little low?

It could be because your most recent payment may have been sitting idle in an Australian Taxation Office (ATO) account, after a technical problem prevented the transfer of a 'significant amount' of payments into super accounts nationwide.

Tens of thousands of small business employees across Australia are thought to have had their super payments delayed for several weeks because of the glitch with a new transfer system.

The ABC has spoken to small businesses who say they were not notified of the problem and only stumbled across it when they noticed their payments had not transferred, or when staff questioned why their monthly super payment had not appeared in their account.

The ATO confirmed the problem but would not provide exact numbers on those affected.

"While the majority of payments were successfully made to employees' accounts, a significant number of the payments were not able to be processed by superannuation funds," the ATO said in a statement.

"Therefore the payments were delayed in reaching employees' superannuation accounts."

Altogether, 300,000 small businesses use the Small Business Superannuation Clearing House (SBSCH) to process superannuation "guarantee" payments to staff.

The Department of Human Services (DHS) was responsible for the service until February when the clearing house was transferred to the ATO.

The move was designed to provide a more secure data platform and better integration with the agency's services.

The suggestion the move would provide a "more secure" data platform has caused some businesses to question how vulnerable the DHS was.

ATO notice 'impossible to find'

Tax agent Clyde Hudson runs a small business with two staff and said the problem started when the new system was implemented — but he was not informed of the issue.

"I first came across it on the 4th of April when we processed one of our employees' payment for super guarantee levy," Mr Hudson said.

Some small businesses reported problems in late March. ( ABC News )

"It hadn't gone through by the 5th of April so I contacted the tax office to see whether they had received the funds, and that's when I found out they'd been having problems with the small business superannuation clearing house."

Mr Hudson said after he questioned the problems, he found out it had been going on since March 23.

"So that's coming up three, nearly four weeks, of employees' superannuation being paid into the tax office and not being transferred to their superannuation fund.

"As tax agents we haven't been told anything, and they eventually directed me to a notice on their web page, but it's not a page people would normally go and find … I then tried to go back to it and it was almost impossible to find," he said.

"As far as I'm aware, they have not contacted individual employers or tax agents."

Penalty fears for missed payments

Online complaints to the ATO's website show the issue began for some small businesses in early March.

Mr Hudson said there had been no suggestion interest which would have otherwise been earned in employee accounts would be paid out.

Small businesses have told the ABC they were not notified of the problem. ( ABC News )

He said the issue also prevented him from making quarterly superannuation payments to staff, as required by law.

"The problem you have is we've lodged one set of payments for processing, but because that hasn't been processed, we now can't lodge the main superannuation payments for the quarter," Mr Hudson said.

"If that payment doesn't go through on time under the act, I as an employer will be penalised for not making a payment on time."

We're prioritising payments: tax office

In a statement, an ATO spokesperson said it had prioritised fixing the problem.

Tens of thousands of employees had their superannuation payments delayed. ( Thinkstock: iStockphoto )

The agency said it took 10 days to process 70 per cent of payments and 95 per cent were processed within 20 days.

As of April 11, about 19,000 individual payments — or 5 per cent — had been delayed for more than 20 days.

"We can now advise that outstanding payments are being progressively released by funds," the statement read.

"We provided general advice on the ATO website about system issues on the SBSCH system status page on March 21. We updated this material on April 11 to provide further information on the system issues."

The ATO said it was hoping to transfer the remaining payments by the close of business on Friday.