One of Canberra's top My School performers has attributed much of its success to a reading program that has survived the coming and going of experimental programs for decades.

Covenant College in Gordon is shown as a top performer in Saturday's league tables, which use the Index of Community Socio-Educational Advantage (ICSEA) to rate Canberra schools against other similar schools around the country.

The kindergarten to year 10 Christian co-educational school topped the year three reading, spelling and grammar lists, and topped every area except numeracy in the year 9 tables.

Principal Martin Keast said the success was being welcomed by students, teachers and parents, but he cautioned that his was a small school of 140 and its fortunes could fluctuate each year.

''It's a small school, so there's a big statistical swing. If we have a class of 10 and a kid in there who is not so able, it can drag you down 10 per cent,'' Mr Keast said.

''But in this case, things are going well and our parents are pleased.''

Mr Keast believed the school's performance in reading, writing, spelling and grammar was based on its adherence to a structured phonics program that has been a foundation for school reading since the 1950s.

''I believe reading is foundational; if you can't read you won't access the other subjects. There's been some strange theories that have come and gone over the years, some of which I think have done a lot of harm, so I'm encouraged that this approach seems to be working.''

The ACT branch of the Australian Education Union hit out at the publication on Friday of My School tables, describing them as ''unreliable and meaningless''.

Acting branch secretary Glenn Fowler said ''schools are jumping around all over the place. In year 3 writing, one school went from 1st last year to 66th this year, whilst in year 3 grammar another school went from 81st to 4th.''

Mr Fowler said the AEU accepted some schools have achieved progress in areas that are tested through NAPLAN, but he said the rankings were affected mostly by the strength of each year's student group.

''The simple fact is that student cohorts change every year. And the smaller the school, the greater the chance of wild fluctuations,'' he said.