SINGLE Touch Payroll reporting became mandatory on July 1 and small businesses had until September 30 to make the transition but the ATO says businesses in the Scenic Rim, Logan and the Redlands have failed to make the deadline.
The ATO said an estimated 539 small businesses were operating in the Scenic Rim but only 313 were on board with STP reporting after the deadline passed.
In the Redlands only 649 out of 925 small businesses had transitioned to STP.
Out of Logan's 321 businesses, 138 had failed to meet the deadline
The law required all small employers with 19 employees or fewer to start reporting through STP by September 30 but ATO assistant commissioner Jason Lucchese said there was still time for businesses to start reporting if they had not already done so.
"If you are a small employer and not sure where to start, there are three possible pathways to take," Mr Lucchese said.
"You can start reporting now through an STP-enabled solution that is right for you, consider if you are eligible for a quarterly reporting concession or apply for a deferral if you need more time.
Mr Lucchese said it was important for small employers to contact the ATO if they had any concerns about their ability to transition to STP.
"You can also speak with your registered tax or BAS agent if you have one," he said.
"We want the transition to STP to be simple and manageable for all employers, and no penalties will be applied in the 2019-20 financial year for small employers who make a genuine attempt to transition or for missed or late reports."
In a Beaudesert Times article in October ATO Assistant Commissioner John Shepherd reassured smaller employers that a number of different STP reporting options would be made available to them, including low cost and simple STP reporting solutions.
"The ATO works closely with small businesses and we are aware of the many competing pressures they face. We will work with all stakeholders on alternative options for those businesses who do not use payroll software," he said.
Mr Shepherd said the majority of businesses in Beaudesert were small firms with fewer than 20 employees, making them an important part of the local economy.
"Importantly, as a result of businesses transitioning to STP reporting, the ATO now has access to employee superannuation data allowing it to better protect employee entitlements," he said.
"For employers it prevents them inadvertently falling behind in payments and ending up with an end-of-year tax debt.
The ATO said it would continue to work with small employers to understand any barriers they may be facing and provide support to help them transition to STP reporting.
The ATO has also developed an online quiz to assist small employers understand their options and determine what the next step should be.
For more information about STP visit ato.gov.au/stp.