Some states are considering a return to pencil and paper after technical glitches hampered the roll out of online NAPLAN testing.
With some students losing connectivity and others unable to log in at all, Australia's educational authorities will meet to work through the fallout.
"It simply isn't good enough that some students have been unfairly disadvantaged by the incompetence of federal authorities," Victorian Education Minister James Merlino said on Wednesday.
"Despite states and territories raising numerous concerns about the test - the federal Liberal government and ACARA have created this chaos."
Outages also affected students in Western Australia according to the state's education director general Lisa Rodgers.
"These are very big issues and we're getting the calls from schools in terms of support in regards to access to the tests," she said.
The Australian Curriculum Assessment and Reporting Authority (ACARA) and representatives from the state and territories will meet on Thursday.
"This group will be considering the implications of connectivity issues experienced by some students on day one and any next steps required," an ACARA spokesman said.
The authority says another 400,000 online tests were successfully submitted on Wednesday and the cause of Tuesday's connectivity issues is still being investigated.
Australian Education Union president Correna Haythorpe said on Wednesday the worst affected states were South Australia and Victoria.
"It is clearer than ever NAPLAN is in no way fit for purpose and that the farcical move to NAPLAN online has been hasty and ill-conceived," Ms Haythorpe said in a statement.
"After last year's debacle with the delivery of NAPLAN online, Federal Education Minister Dan Tehan had the opportunity to institute a full review of NAPLAN. However he failed to do so."
But Mr Tehan said more than 350,000 online tests were successfully submitted on Tuesday and every state and territory agreed to the transition in 2014.
"There are procedures in place to manage issues and tests can be paused, resumed and rescheduled so that all students have the opportunity to complete NAPLAN testing," he said.
"Online delivery of NAPLAN brings significant benefits including better and more precise assessment."
Schools and students participating in the online test can switch to paper tests if needed.
NAPLAN results for each school are published on the My School website, that helps parents and educators assess the performance of schools.
