More than half of all 14-year-olds have not reached expected standards in basic numeracy and literacy, it has emerged.
The report looked at whether pupils were meeting expected standards
A report into children's competence in English and maths in primary and early secondary school does however show good results at several stages in primary.
The Scottish Survey of Achievement was introduced last year and replaced the 5-14 national tests.
A sample of pupils from primary three to S2 took part in the Scottish Executive survey.
The results show whether pupils are reaching expected standards for their age in literacy and numeracy.
Half of primary three pupils were a year ahead at reading, but other results for literacy and numeracy were disappointing.
Most notably, more than half of all S2 pupils were not firmly at the expected standard for their age.
The report showed that just under 50% of pupils had either very good or well established attainment in numeracy and reading.
In P7, more than three-quarters of pupils were achieving expected levels in numeracy and just under three-quarters in reading, again with many achieving numeracy and literacy levels above their age.
Education Minister Peter Peacock said: "While I am pleased that not only are most achieving success at the level expected for their age, many are performing at levels above that expected of their age.
"The survey also confirms past evidence that a greater proportion are reaching the expected levels in primary than in S2.
"It is for precisely that reason that we are recruiting more teachers to reduce class sizes in English and maths to 20 in S1 and S2 and give stronger support for learning at this crucial stage of transition for pupils."
Council umbrella group the Convention of Scottish Local Authorities (Cosla) echoed the minister's statement.
Cosla education spokesman Ewan Aitken said: "It highlights some real success stories, particularly in our primary schools.
"It also confirms what we already knew - that there is more work to be done when children move into secondary education."
He added that there was increasing emphasis on the transitional phase between primary and secondary and on personalised learning, which would help ensure the needs of all children were being met.
Scottish National Party education spokeswoman Fiona Hyslop said the executive's failure to cut class sizes left too many children behind in schools.
She said: "It is extremely worrying that about a third of S2 pupils are not achieving expected levels in literacy and numeracy.
"The problem is that the target of cutting class sizes in English and maths for S1 and S2 pupils is not being met. We must find out now why more teachers are not being employed in the classroom."
Scottish Conservative education spokesman James Douglas-Hamilton said the survey included only a random sample of children in half of Scotland's local authorities.
He said the current education system did not address the needs of every child in Scotland, adding that the country had the fifth highest proportion of young people not in education.
"The statistics we are able to access do not make pleasant reading for anyone," Mr Douglas-Hamilton said.
"Almost a quarter of P7 pupils are not meeting the required standard for numeracy and over a quarter are not meeting the required standard for reading.
"In S2, more than half of 14-year-olds are not achieving expected levels for literacy and numeracy."