The release of the final 2016 NAPLAN results round out a trio of report cards on Australian students and the grade is not great.
But students from non-English-speaking backgrounds have performed strongly in reading and maths.
Results show in Year 3 reading, students from migrant backgrounds had stronger mean scores across all of Australia, and scored more highly in all states except Victoria and the territories.
Migrant children also outscored non-migrant children in Year 3 writing, grammar and punctuation, and numeracy.
The NAPLAN results show there was a continuing strong performance among children from non-English-speaking backgrounds in Years 5, 7 and 9.
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There has also been a definite improvement among Indigenous primary school students, according to NAPLAN results, but there's still a long way to go.
Association of Heads of Independent Schools national chairwoman, Karen Spiller, said the 2016 NAPLAN Report delivered encouraging news for schools working with Aboriginal and Torres Strait Islander students.
She said the 2016 NAPLAN results showed overall gains for Indigenous students in Year 3 and Year 5 in reading and numeracy and welcome improvements in early learning.
Federal Education Minister Simon Birmingham told ABC News 24 the improved results for Indigenous and migrant students were "good news".
"If there is a glimmer of light in today's NAPLAN results, it is that we are seeing in some measures Indigenous students starting to close the gap, that that gap has shortened or narrowed in terms of Year 3 reading skills for Indigenous students," he said.
"Similarly we are seeing in some migrant groups or students that don't have a background in English improvement in their results, in some cases outstripping other students.
"There are positive indicators there that back the fact that we want to see funding distributed according to need."
However the results were less rosy for Australian students in general, with both the literacy and numeracy results confirming that student achievement has largely stagnated in recent years
Education ministers meet on Friday to discuss a new deal on school funding, expected to be finalised in the first half of next year and start from 2018.
Results have improved since NAPLAN testing began in 2008 and there are good results in some year levels in some states and territories, testing administrator, the Australian Curriculum and Reporting Authority says.
But chief executive Robert Randall said with no significant improvements across the board in recent years, Australia should expect more for its children.