Testing was halted suddenly on Wednesday morning after students and teachers were unable to access the writing component of the annual assessment online.
Teachers are calling for the assessment to be scrapped altogether, after many schools were forced to postpone the re-taking of tests.
NAPLAN was riddled with problems and should be replaced with assessments led by teachers in the classroom, a national teachers' union said.
"Today's outages coupled with the high-stakes nature of the assessment risks increasing student anxiety and will add to teachers' increasing workloads," Australian Education Union federal president Correna Haythorpe said.
"There will also be questions about the accuracy of the NAPLAN results once these assessments finally take place."
The federal opposition's education spokesman questioned the validity of the data collected on Wednesday and said the minister responsible should explain how the problems will be rectified.
"Tonight there will be 1.4 million young people asking their parents questions about today's abandoned NAPLAN tests and what it means for them," Julian Leeser said.
"This also creates deep systemic problems. This failure could skew the entire dataset."
The Australian Curriculum and Assessment Reporting Authority (ACARA) confirmed the outage affected students trying to log in to the online test portal.
Grade 3 students were not impacted because their assessment is completed by hand.
"This issue is being urgently investigated by our technology provider, Education Services Australia, who run the platform," ACARA said in a statement.
More than 1.3 million students in grades 3, 5, 7 and 9 were set to begin testing on Wednesday, although the full extent of the outage is not yet clear.
An authority spokesperson confirmed testing had resumed after 12pm on Wednesday after issues relating to the online portal were fixed.
"We apologise for the disruption to students and schools, and thank them for their patience," the spokesperson said.
"The issue has now been resolved and schools have been informed they can resume testing."
Educators took to social media to describe the confusion and interruptions following the widespread outage.
A Victorian secondary school teacher told AAP the disruption was difficult to manage, with students left nervous and unsettled by the outage.
They hope NAPLAN would return to pen and paper.
The national assessment - which tests reading, writing and language conventions, along with numeracy - transitioned to a fully online format in 2022.
NSW's education standards authority Paul Martin confirmed students across the state had reported the online portal being slow.
"Some students were able to log on and some weren't. It reached a point where ACARA provided advice to all schools to pause the test," he said.
NSW Education Minister Prue Car asked students and parents not to panic, confirming there was a wide window to undertake the testing.
Victorian Curriculum and Assessment Authority chief executive Andrew Smith reported many students had been experiencing difficulty on Wednesday morning.
Schools that did not experience troubles continued testing as planned.
"We don't have actual numbers yet, but it would seem that there's enough schools for us to be concerned," Mr Smith told ABC Melbourne.
Victorian exams have been plagued by blunders in recent years.
In 2024, a mistake allowed pupils to access questions in advance from instructional cover sheets at the front of online booklets.
The debacle affected 65 of 116 Victorian Certificate of Education exams and led to the sacking of the state curriculum and assessment authority's entire board following a review.
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