As of midday, nine out of 10 people trying to file tax returns online were succeeding, according to the Australian Taxation Office.
The ATO's online systems have been struggling to cope with post-EOFY demand.
"We're sorry for any inconvenience that issues with our online systems have caused," said a statement issued this afternoon by ATO second commissioner Geoff Leeper.
"We're really disappointed that some people are still experiencing some slowness, because you’ve told us we have a great product in myTax. People that are successfully lodging are telling us how quick and easy it is."
Leeper said that lodgements to date are on par with last year.
As of yesterday, the ATO had received 300,000 tax returns, including 71,000 through myTax and 47,000 through eTax.
"If it's not urgent for you to lodge now, we suggest that you wait until August when there will be more pre-fill data available to enhance your experience, making it easier and quicker," Leeper said.
The processing time for electronic tax returns has not been impacted by the problems plaguing myTax, the ATO said.
"We are working 24 hours a day to fix this issue and have many staff dedicated to this project. This is our number one priority right now," a statement issued by the agency yesterday said.
"While some people are successfully lodging online, we know some people continue to experience issues with our services, including navigation between pages, slow response times and other concerns," the statement said.
Shadow assistant treasurer Andrew Leigh described the performance of myTax as "pretty disappointing".
"We have the tried and tested eTax system which is being phased out and the poor ATO staff — after 4700 job cuts — are now being asked to deliver this new myTax system," Leigh said in an interview today with ABC News Radio's Steve Chase.
"They've got an IT system that really seems to be struggling to keep up. I don't blame the tax office. I blame a government which expects agencies to roll out new systems while slashing the public service."