The federal government has rejected criticism from the coalition about the costs of the superannuation clearing house service, saying the opposition has used the wrong figures in its calculations.

On Friday, opposition treasury spokesman Mathias Cormann and opposition small business, competition policy and consumer affairs spokesman Bruce Billson argued Australian taxpayers had to pay $177 for every transaction due to the low number of registrations for the service.

This amount was based on a cost of $16 million a year, but Small Business Minister Nick Sherry said the quoted cost in the budget was actually over a three-year period.

"It's no surprise the coalition keeps making mistakes with figures - they don't cost their policies and can't read budget papers," Sherry said yesterday.

"They're being their usual negative selves - knocking an excellent service that is growing in popularity by the day."

Financial Services and Superannuation Minister Bill Shorten said the clearing house had received good feedback from businesses that had used it.

"The response from those using the service has been truly remarkable - 99 per cent of them say they would recommend it to other small businesses," Shorten said.

"Yet, the coalition wants to spend up to $368 million of taxpayers' money to set up a duplicate scheme."

The clearing house service was introduced on 1 July 2010 and businesses can access system, which is run by Medicare, free of charge.

According to the government, around 4500 employers had registered with the service as of 15 June, 30,000 employees had been added to the system and almost 90,000 employee payments had been made totalling close to $50 million.