It’s the second year in a row the country has missed its annual climate change goal, despite achieving cuts in actual emissions.
The failure has been blamed on the way progress towards the targets is quantified.
There are two measures of greenhouse gases - source emissions, which represent the actual levels of climate-warming gases released, and adjusted emissions, which take account of the Europe-wide emissions trading scheme and are used to measure progress against targets.
Scotland’s adjusted emissions for 2017 were 46.4 million tonnes of carbon dioxide equivalent - a rise of 3.7 per cent from the previous year.
Source emissions of seven climate-warming gases totalled 40.5 million tonnes of carbon dioxide equivalent - 3.3 per cent lower than the 2016 figure.
This means Scotland has officially cut emissions by 39.1 per cent from the 1990 baseline level.
However, source emissions have dropped by 46.8 per cent.
Scottish laws demands emissions reductions of at least 80 per cent by 2050, with an interim target of 42 per cent by 2020.
The 2020 goal was exceeded in 2014 and 2015, but the increase in adjusted emissions means it was missed in 2016 and 2017.
Scotland’s environment secretary Roseanna Cunningham expressed disappointment, but insisted climate change would remain a top priority.
“We are facing a global climate emergency, and we must all act accordingly,” she said.
“The Scottish Government is already looking across our whole range of responsibilities to make sure we continue with the policies that are working and go further, faster, wherever possible, and we’ve been clear that climate change will be at the heart of our next Programme for Government and Spending Review.
“These statistics show that there can be no room for complacency. If Scotland is to end its contribution to climate change we cannot shirk from the challenge, and we tackle it together.
“Difficult decisions will have to be made but Scotland is not in the business of taking the easy way out - we are up for the challenge.”
Environmentalists say the latest figures show action to reduce emissions must be stepped up, particularly in areas such as transport, domestic heating and agriculture.
Caroline Rance, from the coalition Stop Climate Chaos Scotland (SCCS), said: “Scientists have told us that we need to move faster, and in April the First Minister declared a climate emergency.
“This means acting with even greater urgency to cut emissions now and over the next decade.
“MSPs must ensure that the new Climate Change Bill, which they will be voting on in Parliament next week, includes tougher climate targets and strong policies to slash emissions.”
Mark Ruskell, environment and climate spokesman for the Scottish Greens, said the figures show the Scottish Government “has much work to do” to fulfil its world-leading climate ambitions.
“These figures must act as a wake-up call,” he said.
“Business as usual is no longer acceptable. The Scottish Government needs to urgently accelerate investment in improved public transport and safer walking and cycling routes to give people a real alternative to the car.”
Scottish Liberal Democrat energy spokesman Liam McArthur accused the government of complacency.
He said: “SNP ministers have boasted about meeting their emissions targets. This report, however, shows that Scotland has had five years’ progress knocked back in a single year.
“The First Minister may have declared a climate emergency but the situation is getting worse not better.”