State government data reveals 12.07 per cent of Queensland Treasury bills were paid late in the September quarter, more than double the rate last year.

In the September quarter, Treasury paid 160 small and large businesses late, with the bill totalling $1.45 million.

Overall, 1300 payments were made by Queensland Treasury, worth $26 million.

Queensland Treasury is responsible for managing Queensland's finances, supporting economic growth and preparing the state budget.

Queenslanders are stung with fees for late payments to the state government, such as $63.85 for renewing car registration after the due date, and unpaid fines registered with the State Penalties Enforcement Registry attract a registration fee of $69.80.

LNP leader Deb Frecklington said Treasury should set an example by paying its bills on time.

"The Palaszczuk Labor government should not be treating small businesses like a bank," she said.

Ms Frecklington said the LNP had committed to paying small businesses with government contracts within 20 calendar days for contracts up to $1 million.

The state government has a policy of paying penalty interest to small business for all bills on contracts up to $1 million paid later than 30 calendar days.

It was understood no applications for interest payments were made to Treasury.

The Department of Premier and Cabinet recorded a rate of 11.11 per cent late payments for the September quarter, Justice and Attorney General was 3.5 per cent and the Department of Aboriginal and Torres Strait Islander Partnerships was 5.04 per cent.

A Treasury spokesman said a range of "administrative issues" in August and September resulted in an unacceptable number of late payments during the September quarter.

"This is an extremely unusual circumstance; an average of payment data between January 2016 to the start of the September 2018 quarter shows around 95 per cent of debts were finalised by Queensland Treasury within the month they were received," he said.

The spokesman said Queensland Treasury had implemented several process changes and was confident the issues had been resolved and payments would return to previous levels.

Chamber of Commerce and Industry Queensland spokesman Dan Petrie said many businesses were operating on razor-thin margins and not being paid could put them at risk of going out of business.

"When businesses don't get paid on time, employees suffer, investment in plant and equipment suffers, stress goes through the roof," he said.

"It's simply not good enough with the resources they [the government] have."

Mr Petrie said it was a disincentive for businesses to bid for government work if there were a question mark about payment times.