More than a third of pupils in their second year at high school are failing to meet numeracy standards.
Official figures have revealed 35% of teenagers in S2 are “not yet working within the level” expected – 2% worse than in the last study in 2011.
The findings showed a considerable decline from P7, where just 2% of youngsters are not making the expected grade.
The performance of primary four and seven pupils has also worsened.
According to the Scottish Survey of Literacy and Numeracy (SSLN) the proportion of children doing well or very well dropped from 76% to 69% in P4 and from 72% to 66% in P7.
The proportion of those pupils performing well or very well from the least deprived areas was 28% higher than from the most deprived areas.
Scottish Conservative education spokeswoman Mary Scanlon said: “These statistics are proof that all is not well in Scottish education when it comes to the matter of improving literacy and numeracy.
“The fact there remains a significant drop in competency between primary and secondary school is a real worry and it is also the reason for the large attainment gap between different groups of pupils.”
Labour MSP Kezia Dugdale said the results should be a wake-up call for the Scottish Government.
“These figures are concerning as they show a marked drop in the proportion of children who are performing well in numeracy at primary school, and no improvement at S2 level,” she said.
Minister for Learning Alasdair Allan said there was clearly a problem in S2 as he announced an extra £1million for schools.