Ministers have voiced concerns after a survey suggested less than half of second year pupils were reaching the expected reading and numeracy levels.
Some attainment levels for S2 caused concern
The Scottish Survey of Attainment looked at how children were performing in primary school and their first two years of secondary school.
Education Secretary Fiona Hyslop said primary school pupils were doing well.
But she added: "I am concerned by the standards of achievement in second year."
The minister said most Scottish pupils were receiving an education which provided them with a good basis to learn in the future.
"There is room for improvement and I am determined to see standards raised in classrooms across Scotland," she said.
"By getting education right in the first few years, we can provide the firm foundation on which to build successful futures."
Former education minister and Labour MSP Hugh Henry said: "There is clearly a problem with the transition from primary school to secondary.
"S2 figures in particular show that they are not adapting to secondary school the way they should and learning is suffering as a result."
Mr Henry said he was confident that measures introduced by his party to tackle the problem would pay off in the future.
Conservative schools spokeswoman Liz Smith said there was "serious concern" over the high percentage of pupils not achieving the basic standards in the three Rs.
"Nothing in our children's education is more important than the basic skills of reading, writing and numeracy," she said.
"Pupils, parents and teachers all agree. All our students must be given every chance and assistance to reach the required standards."
The survey took a snapshot of about 27,000 pupils in P3, P5, P7 and S2 in some 1,300 schools in May and June last year.
It said there were strong levels of attainment for reading, writing and numeracy in P3 and P5.
About two thirds of P7 pupils were well-established or better in numeracy, although the performance was less strong in reading.
Almost 50% were well-established or better in reading at the expected level, with 25% reading at the level expected for S2.
Almost 20% of S2 pupils were well-established or better at the highest level in reading and numeracy.
However, only about 45% had reached expected levels in those subjects.