Average class sizes in P1-P3 have gone up from 22.5 in 2011 to 22.6 in 2012 despite an SNP commitment to reduce them.
The percentage of these pupils in class sizes of 18 or fewer – a key SNP election target – has also dropped, from 20.2% in 2011 to 18.8% in 2012.
Larry Flanagan, general secretary of the Educational Institute of Scotland teaching union, said the rise in class sizes remained an "issue of real concern".
He said: "Experience has shown that only legislation can guarantee lower class sizes in Scotland's schools and we would welcome moves to lower primary class sizes through legislation."
Opposition politicians also went on the attack, with Labour's Hugh Henry accusing the Government of breaking its promises.
He said: "The figures show the shocking reality of the SNP's broken promise on teacher numbers."
Liz Smith, of the Scottish Tories, added: "Every time the Scottish Government has been asked to explain the class-size situation it will only say very good progress is being made, but the reverse is happening."
And Liam McArthur, for the Scottish Liberal Democrats, said the figures "read like a list of broken promises".
However, Eileen Prior, executive director of the Scottish Parent Teacher Council, blamed councils for the increase in class sizes. She said: "Local authorities are clearly not responding to Government pressure on this issue."
Education Secretary Michael Russell highlighted a number of more positive trends from the Government statistics, published yesterday.
Almost all pupils in the first year of primary are now in class sizes of 25 or fewer after the Government passed legislation to enforce the maximum.
And the total number of teachers in Scotland has remained stable at 51,400 after several years where numbers have fallen.
Mr Russell said: "We have almost wiped out P1 classes of more than 25 and we have made clear progress since introducing legislation. We are providing stability in our classrooms and have halted the decline in teacher numbers evident since 2007.
"Small class sizes are a vital part of our commitment to the early years, so where pupil numbers are rising I anticipate councils will increase teacher numbers in future."
But Greg Dempster, general secretary of the Association of Headteachers and Deputes in Scotland, which represents senior primary staff, called for greater flexibility for schools.
He said: "For some time we have been arguing for a policy that would see schools staffed based on agreed maximum pupil-teacher ratios, with flexibility then given to schools to organise classes in the best interests of the pupils."
In the SNP's 2007 election manifesto, the party pledged to cut class sizes to 18 for children in the first three years of primary education. In 2010 the Scottish Government unveiled new regulations to introduce a legal limit of 25 for primary one classes across Scotland.
l The proportion of nursery pupils who have access to a qualified teacher has risen slightly over the past year.
Statistics show 75.4% of pre-school children were taught by a registered teacher in 2012 compared to 74.9% the previous year.