Four papers which provides analysis of the 2019 school test results were published at 8pm on Thursday.
Figures show the rate and number of pupils getting passes in core Higher classes dropped significantly - in some cases by almost as much as 10% at grades A to C.
Scottish Conservative education secretary Jamie Greene said: "This is a snide and cynical move by an SNP Government which is increasingly in crisis across all of Scotland's public services.
"There are clearly major and systematic problems within our education system that the SNP simply refuses to acknowledge or take action on.
"John Swinney insisted there were no issues concerning the drop in pass rates, but this snuck-out report proves him wrong.
"His continuous 'nothing to see here approach' is simply untenable.
"The SNP is failing an entire generation of our children and our once world-leading education system is increasingly losing the faith of parents, pupils and teachers."
A total of 1,515 fewer pupils passed their Higher English exam - a reduction of 5.5% on the previous year and the lowest number since 2014.
Passes dropped by 8.8% - or 178 students - for those sitting Advanced Higher exams in the subject.
Higher maths saw the pass rate fall by 2.1% - the first decline since 2014 - while Higher history pass rates plunge by 14.6% overall and by 10% in A-C grades.
Advanced Higher maths saw the number of passes increase by 1.6%.
Sciences had total passes up 1.6% at a Higher level, with subjects including chemistry, physics, biology and human biology.
Those sitting the subjects at Advanced Higher - not including human biology - saw the number of passes fall by 14.1%, although there was a 13% reduction in those sitting the tests.
Speaking after the publication, Education Secretary John Swinney said: "The Scottish Government regularly monitors and analyses performance to inform decision-making.
"Taken together, this analysis demonstrates good progress in a number of areas and that it is challenging to identify significant drivers of change or to draw firm conclusions about some subjects due to small numbers of entries.
"The analysis has however identified areas that justify further exploration and highlight actions that have been agreed.
"My key areas of focus are to ensure that curriculum and assessment are aligned, how to better support professional learning and development, and maintaining a clear focus on enhancing learning and teaching.
"I will continue to do that in my regular discussions with partners on performance."