It is 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 amounted to 40.5 million tonnes of carbon dioxide equivalent – 3.3 per cent lower than the 2016 figure.
This means Scotland has officially reduced emissions by 39.1 per cent since 1990.
However, source emissions have dropped by 46.8 per cent.
Scottish laws demands emission cuts 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.
“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.”