The biggest teaching union, the EIS, said the results had to be seen in the context of budget cuts that had made classes bigger while squeezing staff numbers and other resources.
The 2014 Scottish Survey of Literacy and Numeracy found
47 per cent of S2 boys were doing well, very well or beyond the level they were being assessed for in writing, a drop of 11 percentage points since 2012. For girls in S2, the equivalent figure was 63 per cent, down from 70 per cent.
In schools in the most deprived communities, 41 per cent of S2 children were found to be in that category for writing, compared with 54 per cent in the last survey.
In the least deprived areas the level also fell, to 64 per cent from 74 per cent, while overall 55 per cent of S2 pupils were said to be doing well or better at writing against 64 per cent in 2012.
In reading the picture was also worse, with 80 per cent of S2 pupils doing “well or very well”, down from 84 per cent in 2012. Performance was also poorer in primary schools.
Ms Constance admitted the results were “not as good as they should be” and said the government would act on its findings.
A new national improvement framework will be set up and Education Scotland inspections will focus on literacy. More learning resources will also be made available to teachers, she said.
“Literacy and numeracy are vital skills for our young people. That’s why the survey was commissioned – to get a clear picture at various stages of school.”
Larry Flanagan, general secretary of the EIS, said: “While it is important to analyse these findings and learn any lessons, the EIS is very clear that particular challenges remain for schools, teachers and pupils.
“For example, we have seen a drop in teacher numbers, a rise in class numbers, teacher workload at an unsustainable level and restrictive budget cuts reducing resources.
“Both local and national government need to realise that austerity has an impact on our schools and young people.”
The literacy survey was carried out a year ago, covering 10,000 pupils and 2,250 schools.