Most Canberra primary schools failed to improve their students' literacy and numeracy at the same rate as other schools around Australia.
And two government high schools' students actually had worse writing scores in year 9 than they did two years earlier when they were in year 7.
The 2016 NAPLAN results of about 9500 Australian schools were released on the My School website on Wednesday.
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Fairfax Media analysed how ACT schoolchildren's results had improved since those same students were last tested in 2014.
While 25 Canberra schools recorded gains above the national average between years 3 and 5, the progress in 66 primary schools was below average.
In numeracy, in the same year group, 32 were at or above the national average rate of improvement and 59 below.
In reading, between years 7 and 9, 15 schools were above the national average and 21 below. For numeracy, 16 schools were at or above the average and 20 below.
Many schools had raw scores above the national average, meaning it was harder to record high gains. Some schools were too small or new to be included in the data.
Government schools that demonstrated above average gains in reading and numeracy between years 3 and 5 included Charnwood-Dunlop School, Richardson Primary, Gowrie Primary, Macquarie Primary, Forrest Primary, Campbell Primary, Giralang Primary, Evatt Primary, Gilmore Primary and Fraser Primary.
Blue Gum topped the list for reading gains among all sectors for the same cohort. Orana Steiner and Burgmann Anglican School revealed improvements in reading and numeracy between years 3 and 5.
St Benedict's Primary and St Clare of Assisi Primary were Catholic schools to note improvements in reading and numeracy between years 3 and 5. Several others, including Holy Spirit Primary and St Thomas the Apostle Primary, made improvements in either subject.
In high school, between years 7 and 9, independent schools came out on top for improvements made. Emmaus Christian School topped the list for improvement in reading and also received above average gains in numeracy. Trinity Christian School made the highest gains in numeracy.
Melba Copland Secondary came second in both instances. Melrose High, Orana Steiner, St Francis Xavier College, Mount Stromlo High, Belconnen High, Harrison School and Alfred Deakin High featured as making improvements in both subjects.
While making above average improvements in reading from years 7 to 9, Kingsford Smith School slipped backwards in writing results, as did Calwell High.
Education Minister Yvette Berry said both schools were working to improve on their results. Calwell High was providing professional development for staff, she said, while Kingsford Smith School was also providing staff training and working with other schools within its network.
"NAPLAN is one piece of the puzzle when it comes to tracking our students' ability in literacy and numeracy and our schools use many other methods to assess and support students in their learning," she said.
Australian Education Union ACT branch secretary Glenn Fowler said ACT schools were making great strides "and we don't need NAPLAN to tell us that".
"It is pleasing that educators are letting curriculum delivery do the work and not resorting to coaching children to take the tests," he said.
The Australian Curriculum, Assessment and Reporting Authority, which releases NAPLAN results, highlighted 19 ACT schools that demonstrated substantially above average gains among 400 others nationally.
"Our attention and our intention, unashamedly, is to celebrate the good things that are going on in these schools," chief executive Robert Randall said ahead of the release.
"We do believe if we can identify and explain improvement in schools then others can learn from them and we can then generalise from that and promote the extent of gain in schools around the country."
Raw scores, which do not account for the socioeconomic status of students, showed Canberra Grammar, Canberra Girls' Grammar and Garran Primary School dominating in the primary years.
Canberra Girls' Grammar also topped almost every subject in years 7 and 9, topped by Telopea Park School in year 9 numeracy, Covenant College in year 7 spelling and Canberra Grammar in year 7 numeracy, and Radford College in year 9 numeracy.