The percentage of pupils achieving an A, B, or C grade at Higher fell from 76.8 per cent in 2018 to 74.8 per cent this year - a drop that was initially brushed off by Mr Swinney as "annual variation".
But a Freedom of Information request has now revealed the SNP minister privately commissioned a multi-agency analysis of the pass rate to uncover the reasons behind the drop.
In documents seen by The Times, the education secretary met with Education Scotland representatives and council bosses on September 3 to "undertake a fuller analysis of the 2019 SQA results".
Mr Swinney asked them to examine the results in greater depth to "consider what they might suggest about the current health of the education system and also to identify what might be required to help more young people to be as successful as possible".
Speaking in parliament on September 5, Mr Swinney had criticised Tory MSPs for "scoffing" at the falling pass rate.
Liz Smith, the Scottish Conservatives' education spokeswoman, said: "Quite frankly, no-one believed John Swinney when he said that the four year decline in Higher pass rates was down to ‘annual variation’.
“Clearly, it was not. There were more serious concerns and that message was coming to him from both his civil servants and senior officers within the education agencies.
“It was therefore disingenuous for Mr Swinney to try to paint a rosy picture about this year's Higher exam pass rates when alarm bells were ringing within his own office.
"The public, and especially parents, pupils and teachers, have a right to know exactly what is going on.
“I have therefore written to the Cabinet Secretary asking him to publish the full information so that there can be full parliamentary scrutiny.
“Neither the Scottish Parliament nor Holyrood’s Education Committee should be kept in the dark.”
A Scottish Government spokesman said: “Every year, we see annual variation in exam results - that is expected in a high performing education system with credible assessment system.
"This year, three-quarters of Higher candidates gained a pass at A-C.
"We are committed to regular monitoring and understanding of the performance of our education system and the Scottish Government, SQA and Education Scotland are analysing the 2019 exam results to consider any required actions to ensure the best outcomes for learners.
"All of these actions were explained to the Education and Skills Committee of the Scottish Parliament on 27 November and there is nothing new in this material.”
The Scottish Government's international panel of education experts warned in September that the attainment gap in Scottish schools might not see a dramatic reduction for at least 15 years.
While they said there had been progress in closing the gap, sustained progress was required before a “sudden growth spurt” would see it substantially narrowed.